Index

_

_add_weights_from_file() (pyrosetta.rosetta.core.scoring.ScoreFunction method) _add_weights_from_stream() (pyrosetta.rosetta.core.scoring.ScoreFunction method) _Ios_Fmtflags (class in pyrosetta.rosetta.std) _Ios_Openmode (class in pyrosetta.rosetta.std) _Ios_Seekdir (class in pyrosetta.rosetta.std) _is_interactive() (in module pyrosetta) _M_write() (pyrosetta.logging_support.PythonLoggingSink method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.TracerImpl method) _pmatch() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) _read_file() (pyrosetta.rosetta.core.io.silent.SilentFileData method)

_RESULTS (class in pyrosetta.rosetta.core.scoring.sc) _RNA_MatchType_ (class in pyrosetta.rosetta.core.fragment.rna) _rosetta_database_from_env() (in module pyrosetta) _static_type_name() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) _write_silent_struct() (pyrosetta.rosetta.core.io.silent.SilentFileData method)

A

A() (in module pyrosetta.rosetta.ObjexxFCL.format) a() (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering method) a0() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) a1() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) a2() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) a3() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) AA (class in pyrosetta.rosetta.core.chemical) aa() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) aa2idx() (in module pyrosetta.rosetta.core.scoring.saxs) aa2randomCodon() (in module pyrosetta.rosetta.core.chemical.NucleotideTools) aa_composition_setup_file() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) aa_composition_setup_file_count() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) aa_from_name() (in module pyrosetta.rosetta.core.chemical) aa_from_one_or_three() (in module pyrosetta.rosetta.core.chemical) aa_from_oneletter_code() (in module pyrosetta.rosetta.core.chemical) aa_from_resid() (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) aa_ind() (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) aa_matrix() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) aa_penalty() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) aa_str() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) aa_submatrix_energies_retrievable() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) aa_trustworthiness() (in module pyrosetta.rosetta.core.scoring.motif) AACompositionEnergy (class in pyrosetta.rosetta.core.scoring.aa_composition_energy) (class in pyrosetta.rosetta.protocols.fldsgn.potentials) AACompositionEnergySetup (class in pyrosetta.rosetta.core.scoring.aa_composition_energy) AACompositionPropertiesSet (class in pyrosetta.rosetta.core.scoring.aa_composition_energy) AAProb (class in pyrosetta.rosetta.protocols.mean_field) AARepeatEnergy (class in pyrosetta.rosetta.core.scoring.aa_repeat_energy) AASynthesisFitnessCost (class in pyrosetta.rosetta.protocols.evolution) aatype_for_node_state() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) ab_dock_chains() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) ab_fold_tree() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) Ab_TemplateInfo (class in pyrosetta.rosetta.protocols.antibody) abase2() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) ABEGO (class in pyrosetta.rosetta.core.sequence) abego() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) abego_char() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) abego_index() (in module pyrosetta.rosetta.protocols.frag_picker.quota) ABEGO_SS_Config (class in pyrosetta.rosetta.protocols.frag_picker.quota) ABEGO_SS_Map (class in pyrosetta.rosetta.protocols.frag_picker.quota) ABEGO_SS_Pool (class in pyrosetta.rosetta.protocols.frag_picker.quota) abego_str() (in module pyrosetta.rosetta.protocols.denovo_design) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) abego_vector() (in module pyrosetta.rosetta.protocols.denovo_design) ABEGOEval (class in pyrosetta.rosetta.core.fragment.picking_old.vall.eval) ABEGOManager (class in pyrosetta.rosetta.core.sequence) abort_min() (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.Multifunc method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc method) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GriddedAtomTreeMultifunc method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc method) AbrelaxApplication (class in pyrosetta.rosetta.protocols.abinitio) abs() (in module pyrosetta.rosetta.ObjexxFCL) abs_score_convergence_threshold() (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) abs_score_diff_after_minimization() (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) absfpart() (in module pyrosetta.rosetta.protocols.cryst) absolute() (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) absolute_stereochemistry() (pyrosetta.rosetta.core.chemical.Atom method) absolute_vec() (in module pyrosetta.rosetta.protocols.features.strand_assembly) AbstractArchiveBase (class in pyrosetta.rosetta.protocols.jd2.archive) acc_bbg_in_bb_bb_hbond() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) accept() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) accept_counter() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) accept_declined_claim() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) acceptance_rate() (pyrosetta.rosetta.protocols.moves.TrialMover method) AcceptanceCheck (class in pyrosetta.rosetta.protocols.loop_modeling.utilities) accepted_scores() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) AcceptedScores (class in pyrosetta.rosetta.protocols.monte_carlo) acceptor_group() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond method) acceptor_selector() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) acceptor_symmetry_copy_index() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond method) AcceptorAtomFilter (class in pyrosetta.rosetta.core.chemical) accepts() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) accepts_since_last_batch() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) access_Real_MathNTensor() (in module pyrosetta.rosetta.numeric) accomodate_length_change() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) accpt_pos() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) accpt_pos_sc() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) accumulate() (pyrosetta.rosetta.core.scoring.EMapVector method) accumulate_energy() (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) ACHAR() (in module pyrosetta.rosetta.ObjexxFCL.Fortran) actcoord() (pyrosetta.rosetta.core.conformation.Residue method) actcoord_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) activate() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) active() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) active_1benmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationNode method) active_1benmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationNode method) active_1benmeths_ext_begin() (pyrosetta.rosetta.core.scoring.MinimizationNode method) active_1benmeths_ext_end() (pyrosetta.rosetta.core.scoring.MinimizationNode method) active_1benmeths_std_begin() (pyrosetta.rosetta.core.scoring.MinimizationNode method) active_1benmeths_std_end() (pyrosetta.rosetta.core.scoring.MinimizationNode method) active_2b_score_types() (pyrosetta.rosetta.core.scoring.EnergyGraph method) active_2benmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) active_2benmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) active_2benmeths_ext_begin() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) active_2benmeths_ext_end() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) active_2benmeths_std_begin() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) active_2benmeths_std_end() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) active_atom_tree() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) active_constraint() (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) active_intrares2benmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationNode method) active_intrares2benmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationNode method) active_intrares2benmeths_ext_begin() (pyrosetta.rosetta.core.scoring.MinimizationNode method) active_intrares2benmeths_ext_end() (pyrosetta.rosetta.core.scoring.MinimizationNode method) active_intrares2benmeths_std_begin() (pyrosetta.rosetta.core.scoring.MinimizationNode method) active_intrares2benmeths_std_end() (pyrosetta.rosetta.core.scoring.MinimizationNode method) active_residue() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) active_residue_cop() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) active_residue_data() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) active_restype() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) active_restype_index() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) active_score_types() (pyrosetta.rosetta.core.scoring.EnergyGraph method) active_variables() (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.Expression method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression method) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) actual_cycles() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) actual_residue_connection() (pyrosetta.rosetta.core.conformation.Residue method) acyclic() (in module pyrosetta.rosetta.ObjexxFCL.internal.ObserverMediator) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) adaptation_period() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) adaptive() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) adaptive_movers() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) add() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.PCluster method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.utility.options.OptionCollection method) add_a3b_hbs_constraint() (in module pyrosetta.rosetta.core.pose.ncbb) add_acceptance_check() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) add_actcoord_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) add_additional_low_resolution_step() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) add_additional_task_operaration() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) add_adduct() (pyrosetta.rosetta.core.chemical.ResidueType method) add_alanine_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) add_all_atoms() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) add_all_evaluators() (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory method) add_all_model_edges_from_binary() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) add_all_rosetta_options() (in module pyrosetta.rosetta) add_and_initialize_reference_pose() (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) add_anonymous_option() (in module pyrosetta.rosetta.basic.options) add_another_virtual_res() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) add_anti_chi_constraints() (in module pyrosetta.rosetta.core.pose.rna) add_architect() (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) add_as_other_struct_if_relevant() (pyrosetta.rosetta.core.io.silent.SilentFileData method) add_at_ind() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) add_atmname_using() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) add_atom() (in module pyrosetta.rosetta.core.kinematics) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) add_atom_alias() (pyrosetta.rosetta.core.chemical.ResidueType method) add_atom_set() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) add_atom_type_set_parameters_from_command_line() (in module pyrosetta.rosetta.core.chemical) add_atomgeom_evaluator() (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) add_attribute() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) add_attributes() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) add_attributes_for_common_options() (in module pyrosetta.rosetta.protocols.ncbb) add_attributes_for_helix_params() (in module pyrosetta.rosetta.protocols.helical_bundle) add_attributes_for_make_bundle_dofs() (in module pyrosetta.rosetta.protocols.helical_bundle) add_attributes_for_make_bundle_minorhelix_defaults() (in module pyrosetta.rosetta.protocols.helical_bundle) add_attributes_for_make_bundle_other_defaults() (in module pyrosetta.rosetta.protocols.helical_bundle) add_attributes_for_make_bundle_symmetry() (in module pyrosetta.rosetta.protocols.helical_bundle) add_attributes_for_minor_helix_params() (in module pyrosetta.rosetta.protocols.helical_bundle) add_attributes_for_other_helix_params() (in module pyrosetta.rosetta.protocols.helical_bundle) add_backrub_mover() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) add_base_residue_type() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) add_batch() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) add_behavior() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) add_blacklist() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) add_bond() (pyrosetta.rosetta.core.chemical.ResidueType method) add_built_in_options() (pyrosetta.rosetta.utility.options.OptionCollection method) add_c_terminal_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) add_canonical_atom_alias() (pyrosetta.rosetta.core.chemical.ResidueType method) add_case() (pyrosetta.rosetta.core.chemical.Patch method) add_CDR_to_MoveMap() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) add_chain_from_pose() (in module pyrosetta.rosetta.protocols.denovo_design) add_chain_id() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) add_chain_name() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) add_chainbreaks_according_to_jumps() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) add_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) add_chi_constraints() (in module pyrosetta.rosetta.core.pose.rna) add_chi_rotamer() (pyrosetta.rosetta.core.chemical.ResidueType method) add_chi_rotamer_to_last_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) add_choice() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) add_chunk_filter() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) add_chunk_set() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) add_cluster_comments_to_pose() (in module pyrosetta.rosetta.protocols.antibody.clusters) add_cmdline_claims() (in module pyrosetta.rosetta.protocols.topology_broker) add_comment() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.core.io.silent.SilentStruct method) add_common_denovo_architect_attributes() (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) add_components_to_pose_if_necessary() (pyrosetta.rosetta.protocols.matdes.SymDofMover method) add_condition() (pyrosetta.rosetta.protocols.filters.IfThenFilter method) add_conformation_viewer() (in module pyrosetta.rosetta.protocols.viewer) add_connected_resonance() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) add_connection() (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) add_constraint() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) add_constraints() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) add_constraints_from_cmdline() (in module pyrosetta.rosetta.core.scoring.constraints) add_constraints_from_cmdline_to_pose() (in module pyrosetta.rosetta.core.scoring.constraints) add_constraints_from_cmdline_to_scorefxn() (in module pyrosetta.rosetta.core.scoring.constraints) add_constraints_from_file() (in module pyrosetta.rosetta.protocols.dna) add_constraints_to_metal() (in module pyrosetta.rosetta.core.util) add_coordinate_constraints() (in module pyrosetta.rosetta.core.scoring.constraints) (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) add_coordinate_constraints_to_pose() (in module pyrosetta.rosetta.protocols.loops) (in module pyrosetta.rosetta.protocols.relax) add_coordinatecst_for_hotspot_packing() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) add_covalent_linkage() (in module pyrosetta.rosetta.core.util) add_covalent_linkages_to_metal() (in module pyrosetta.rosetta.core.util) add_creator() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) add_ct_name() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) add_current_job_data_to_ss() (in module pyrosetta.rosetta.protocols.jd2) add_cut_bond() (pyrosetta.rosetta.core.chemical.ResidueType method) add_cutpoint_closed() (in module pyrosetta.rosetta.core.import_pose) add_cutpoint_variants() (in module pyrosetta.rosetta.protocols.forge.methods) (in module pyrosetta.rosetta.protocols.loops) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) add_cutpoint_variants_for_ccd() (in module pyrosetta.rosetta.protocols.grafting) add_cutpoints() (in module pyrosetta.rosetta.protocols.denovo_design) add_datum() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) add_delta_omega1_value() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) add_delta_z1_value() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) add_dens_scores_from_cmdline_to_scorefxn() (in module pyrosetta.rosetta.core.scoring.electron_density) add_dependency_to() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) add_design_task() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) add_dist_viol_to_assignments() (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) add_distance() (pyrosetta.rosetta.protocols.contact_map.Contact method) add_DoF() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) add_dof_constraint() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) add_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) add_edges_from_binary() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) add_edits() (pyrosetta.rosetta.utility.options.OptionCollection method) add_energy() (pyrosetta.rosetta.core.io.silent.SilentStruct method) add_energy_edge() (pyrosetta.rosetta.core.scoring.EnergyGraph method) add_evaluated_structure() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) add_evaluation() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) add_evaluator() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) add_evaluator_for_target_restype() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) add_evaluators() (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator method) add_extent_eval() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) add_extent_gen() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) add_external_geom_sampler() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) add_external_geometry_samples_for_constraint() (pyrosetta.rosetta.protocols.match.Matcher method) add_extra_method() (pyrosetta.rosetta.core.scoring.ScoreFunction method) add_fa_constraints_from_cmdline() (in module pyrosetta.rosetta.core.scoring.constraints) add_fa_constraints_from_cmdline_to_pose() (in module pyrosetta.rosetta.core.scoring.constraints) add_fa_constraints_from_cmdline_to_scorefxn() (in module pyrosetta.rosetta.core.scoring.constraints) add_fade_chain_break_constraint_across_gap() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) add_filter() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) add_filter_param() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) add_fragment() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) add_fragment_eval() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) add_fragment_gen() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) add_fragments() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) add_free_peptide_mover() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) add_function_name() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) add_generator() (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) add_grid() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) add_group() (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.task_operations.LinkResidues method) add_groupD() (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) add_groupE() (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) add_harmonic_chain_break_constraint() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) add_harmonic_dihedral_cst_general() (in module pyrosetta.rosetta.protocols.antibody.constraints) add_hbs_constraint() (in module pyrosetta.rosetta.core.pose.ncbb) add_hits() (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) add_hydrophobic_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) add_individual_constraint() (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) add_info_for_csts() (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) add_init_dev_penalty() (in module pyrosetta.rosetta.protocols.mpi_refinement) add_input_job_result_index() (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) add_inputvalue() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) add_job_data_to_ss() (in module pyrosetta.rosetta.protocols.jd2) add_jump() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) add_jump_id() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) add_jump_selector() (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) add_kic_mover() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) add_labels_as_remark() (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) add_leap() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) add_legacyleap() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) add_line() (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.protocols.frags.VallData method) add_linker() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) add_linker_asymmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) add_linker_bonds_asymmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) add_linker_bonds_symmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) add_linker_constraints_asymmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) add_linker_constraints_symmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) add_linker_segments() (in module pyrosetta.rosetta.protocols.legacy_sewing) add_linker_symmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) add_long_range_damping() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) add_loop() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.loops.Loops method) add_loop_flank_residues_bb_to_movemap() (in module pyrosetta.rosetta.protocols.loops) add_loop_segment() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) add_loop_size() (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) add_loops_from_bool_vector() (in module pyrosetta.rosetta.protocols.antibody.design) add_lower_padding() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) add_lower_terminus_type_to_conformation_residue() (in module pyrosetta.rosetta.core.conformation) add_lower_terminus_type_to_pose_residue() (in module pyrosetta.rosetta.core.pose) add_mainchain_segments() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) add_mainchain_segments_from_options() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) add_match() (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) add_mcfi() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) add_membrane_virtual() (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) add_metalbinding_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) add_metapatch_connect() (pyrosetta.rosetta.core.chemical.ResidueType method) add_metric_value_getter() (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) add_model() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) add_monte_carlo_viewer() (in module pyrosetta.rosetta.protocols.viewer) add_motif_bb_constraints() (in module pyrosetta.rosetta.protocols.motifs) add_motif_sc_constraints() (in module pyrosetta.rosetta.protocols.motifs) add_movable_jump() (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) add_movemap_from_loopres() (in module pyrosetta.rosetta.protocols.mpi_refinement) add_mover() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) add_mover_group() (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) add_MPI_rank_handling_message() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) add_msg() (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.utility.excn.BadInput method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) add_mutation_ddG() (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) add_n_terminal_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) add_named_selector() (pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser method) add_new_cluster() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) add_new_data() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) add_new_sequence_into_global_sequence() (in module pyrosetta.rosetta.core.pose.full_model_info) add_node() (pyrosetta.rosetta.utility.graph.Digraph method) add_non_protein_cst() (in module pyrosetta.rosetta.protocols.hybridization) add_nt_seq_to_pose() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) add_nu() (pyrosetta.rosetta.core.chemical.ResidueType method) add_num_neighbors() (in module pyrosetta.rosetta.protocols.legacy_sewing) add_number_base_pairs() (in module pyrosetta.rosetta.core.pose.rna) add_number_native_base_pairs() (in module pyrosetta.rosetta.core.pose.rna) add_numeric_property() (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueType method) add_observer() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) add_observer_cache_segments_to_set() (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) add_onebody_enmeth() (pyrosetta.rosetta.core.scoring.MinimizationNode method) add_oop_constraint() (in module pyrosetta.rosetta.core.pose.ncbb) add_operation() (pyrosetta.rosetta.core.chemical.PatchCase method) add_optional_name_attribute() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) add_orbital() (pyrosetta.rosetta.core.chemical.ResidueType method) add_orbital_bond() (pyrosetta.rosetta.core.chemical.ResidueType method) add_ordered_subelement_set_as_optional() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) add_ordered_subelement_set_as_pick_one() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) add_ordered_subelement_set_as_pick_one_or_none() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) add_ordered_subelement_set_as_repeatable() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) add_ordered_subelement_set_as_required() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) add_other_pose() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) add_other_struct() (pyrosetta.rosetta.core.io.silent.SilentStruct method) add_overall_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) add_overlap_loop() (pyrosetta.rosetta.protocols.loops.Loops method) add_overlap_to_loops() (in module pyrosetta.rosetta.protocols.denovo_design.movers) add_parameters() (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) add_parameters_from_file() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) add_parameters_set() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) add_parent_remark() (pyrosetta.rosetta.core.io.silent.SilentStruct method) add_patches() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) add_pdb_id() (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) add_pdb_ids() (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) add_perturbation_magnitude() (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) add_perturbation_type() (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) add_perturber() (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) add_polar_atom() (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) add_pool() (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) add_pose() (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) add_poseinfo_to_ss() (in module pyrosetta.rosetta.protocols.mpi_refinement) add_position_data() (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) add_postfold_mover() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) add_prefold_mover() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) add_property() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.ResidueType method) add_proton_index() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) add_query_ss() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) add_r1_value() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) add_rcg() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) add_reactivity() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) add_refiner() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) add_relevant() (pyrosetta.rosetta.utility.options.OptionCollection method) add_remark() (in module pyrosetta.rosetta.protocols.denovo_design) add_remodel_constraints_to_pose() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) add_required_connection_for_residue() (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) add_required_connections_between_regions() (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) add_required_name_attribute() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) add_res() (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) add_residue() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) add_residue_connection() (pyrosetta.rosetta.core.chemical.ResidueType method) add_residue_dis() (pyrosetta.rosetta.core.scoring.TMscoreStore method) add_residue_pair_jump() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) add_residue_selector() (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) add_residues_to_pose() (in module pyrosetta.rosetta.protocols.denovo_design) add_reslabel() (pyrosetta.rosetta.core.pose.PDBInfo method) add_reslabels_to_pose() (in module pyrosetta.rosetta.protocols.hbnet) add_restriction() (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) add_reweighter() (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer method) add_ring() (pyrosetta.rosetta.core.chemical.ResidueType method) add_rms() (pyrosetta.rosetta.numeric.model_quality.RmsData method) add_rosetta_options_0() (in module pyrosetta.rosetta) add_rosetta_options_1() (in module pyrosetta.rosetta) add_rosetta_options_10() (in module pyrosetta.rosetta) add_rosetta_options_11() (in module pyrosetta.rosetta) add_rosetta_options_12() (in module pyrosetta.rosetta) add_rosetta_options_13() (in module pyrosetta.rosetta) add_rosetta_options_14() (in module pyrosetta.rosetta) add_rosetta_options_15() (in module pyrosetta.rosetta) add_rosetta_options_2() (in module pyrosetta.rosetta) add_rosetta_options_3() (in module pyrosetta.rosetta) add_rosetta_options_4() (in module pyrosetta.rosetta) add_rosetta_options_5() (in module pyrosetta.rosetta) add_rosetta_options_6() (in module pyrosetta.rosetta) add_rosetta_options_7() (in module pyrosetta.rosetta) add_rosetta_options_8() (in module pyrosetta.rosetta) add_rosetta_options_9() (in module pyrosetta.rosetta) add_rotamer() (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) add_rotamer_into_existing_group() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) add_rotamers() (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) add_rv_info() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) add_sampler() (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) add_schema_restrictions_for_strings() (in module pyrosetta.rosetta.utility.tag) add_score() (pyrosetta.rosetta.protocols.sic_dock.JointScore method) add_score_info_to_pose() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) add_score_line_string() (in module pyrosetta.rosetta.core.pose) add_scoring_method() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) add_secondary_downstream_match_geometry_for_constraint() (pyrosetta.rosetta.protocols.match.Matcher method) add_secondary_upstream_match_geometry_for_constraint() (pyrosetta.rosetta.protocols.match.Matcher method) add_section() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) add_segment() (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) add_segments_for_chain() (in module pyrosetta.rosetta.protocols.denovo_design.components) add_selector() (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector method) add_selector_rlto_pair() (pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions method) add_setup_mover() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) add_sfs_drs_enmeth() (pyrosetta.rosetta.core.scoring.MinimizationNode method) add_shear_mover() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) add_sheet() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) add_sheets_from_pose() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) add_sheets_from_spairs() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) add_sidechain_mc_mover() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) add_sidechain_mover() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) add_similarity() (pyrosetta.rosetta.protocols.cluster.DataPoint method) add_simple_metric() (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) add_simple_subelement() (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) add_single_atom_to_power_diagram() (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) add_single_cutpoint_variant() (in module pyrosetta.rosetta.protocols.loops) add_single_magnesium() (in module pyrosetta.rosetta.protocols.magnesium) add_small_mover() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) add_spanning_region() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) add_special_edges() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) add_state() (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) add_strand_extension() (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) add_strand_pairs_cst() (in module pyrosetta.rosetta.protocols.hybridization) add_string() (pyrosetta.rosetta.protocols.jd2.Job method) add_string_property() (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueType method) add_string_real_pair() (pyrosetta.rosetta.protocols.jd2.Job method) add_string_real_pair_to_current_job() (in module pyrosetta.rosetta.protocols.jd2) add_string_string_pair() (pyrosetta.rosetta.protocols.jd2.Job method) add_string_string_pair_to_current_job() (in module pyrosetta.rosetta.protocols.jd2) add_string_to_current_job() (in module pyrosetta.rosetta.protocols.jd2) add_string_value() (pyrosetta.rosetta.core.io.silent.SilentStruct method) add_strings() (pyrosetta.rosetta.protocols.jd2.Job method) add_strings_to_current_job() (in module pyrosetta.rosetta.protocols.jd2) add_structure() (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) add_structure_replace_tag_if_necessary() (pyrosetta.rosetta.core.io.silent.SilentFileData method) add_subelement() (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) add_subelement_for_parse_stub_sets() (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) add_submotif_info() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) add_submotif_info_from_line() (pyrosetta.rosetta.core.io.silent.SilentStruct method) add_syn_anti_chi_constraints() (in module pyrosetta.rosetta.core.pose.rna) add_syn_chi_constraints() (in module pyrosetta.rosetta.core.pose.rna) add_target_restype() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) add_target_selector() (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) add_task_operation() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) add_task_operations() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) add_template_selector() (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) add_to_allowed_aas() (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) add_to_energy_map() (pyrosetta.rosetta.core.scoring.EnergyEdge method) add_to_multimodel_pdb() (in module pyrosetta.rosetta.core.io.pdb) add_to_nodes_one_body_energy() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) add_to_one_body_energies() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) add_to_one_body_energy_for_node_state() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) add_to_pose() (in module pyrosetta.rosetta.protocols.denovo_design.components) add_to_pose_list() (in module pyrosetta.rosetta.protocols.stepwise.modeler) add_to_weight() (pyrosetta.rosetta.core.scoring.ScoreFunction method) add_top_level_element() (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) add_torsion() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) add_triazole_constraint() (in module pyrosetta.rosetta.core.pose.ncbb) add_twobody_enmeth() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) add_type() (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory method) add_unpatchable_residue_type() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) add_unrecognized_atoms() (pyrosetta.rosetta.core.pose.PDBInfo method) add_upper_padding() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) add_upper_terminus_type_to_conformation_residue() (in module pyrosetta.rosetta.core.conformation) add_upper_terminus_type_to_pose_residue() (in module pyrosetta.rosetta.core.pose) add_upstream_restype_for_constraint() (pyrosetta.rosetta.protocols.match.Matcher method) add_user_provided_mover() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) add_vall_cheating_fragments() (in module pyrosetta.rosetta.protocols.frags) add_vall_fragments() (in module pyrosetta.rosetta.protocols.frags) add_values_from_center() (in module pyrosetta.rosetta.core.chemical.rna) add_variant_type() (pyrosetta.rosetta.core.chemical.ResidueType method) add_variant_type_to_conformation_residue() (in module pyrosetta.rosetta.core.conformation) add_variant_type_to_pose_residue() (in module pyrosetta.rosetta.core.pose) add_variant_type_to_residue() (in module pyrosetta.rosetta.core.pose) add_virtual_O2Prime_hydrogen() (in module pyrosetta.rosetta.core.pose.rna) add_virtual_res() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) add_virtual_residue_to_cterm() (in module pyrosetta.rosetta.protocols.relax) add_virtual_sugar_res() (in module pyrosetta.rosetta.core.import_pose) add_water_overcoordinated_hb_score() (in module pyrosetta.rosetta.protocols.hydrate) add_weights_from_file() (pyrosetta.rosetta.core.scoring.ScoreFunction method) add_whole_pose_context_enmeth() (pyrosetta.rosetta.core.scoring.MinimizationGraph method) AddAllPositionsMPM (class in pyrosetta.rosetta.protocols.match) AddAromaticAtomType() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) AddAtom (class in pyrosetta.rosetta.core.chemical) AddAtom() (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) AddAtomAlias (class in pyrosetta.rosetta.core.chemical) AddAtomType() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) AddBond (class in pyrosetta.rosetta.core.chemical) AddBondType (class in pyrosetta.rosetta.core.chemical) AddCDRProfileSetsOperation (class in pyrosetta.rosetta.protocols.antibody.task_operations) AddCDRProfilesOperation (class in pyrosetta.rosetta.protocols.antibody.task_operations) AddChainBreak (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) AddChi (class in pyrosetta.rosetta.core.chemical) AddChiRotamer (class in pyrosetta.rosetta.core.chemical) AddConnect (class in pyrosetta.rosetta.core.chemical) AddConnectAndTrackingVirt (class in pyrosetta.rosetta.core.chemical) AddConnectDeleteChildProton (class in pyrosetta.rosetta.core.chemical) AddConstraints (class in pyrosetta.rosetta.protocols.constraint_generator) AddGood2BPairEnergyRotamers (class in pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations) AddHelixSequenceConstraintsMover (class in pyrosetta.rosetta.protocols.aa_composition) additional_string_output() (pyrosetta.rosetta.core.io.StructFileRep method) AddJobPairData (class in pyrosetta.rosetta.protocols.simple_moves) AddMembraneMover (class in pyrosetta.rosetta.protocols.membrane) AddMembraneMoverCreator (class in pyrosetta.rosetta.protocols.membrane) AddMembraneSpanConstraintCreator (class in pyrosetta.rosetta.protocols.membrane) AddMembraneSpanTermZConstraintCreator (class in pyrosetta.rosetta.protocols.membrane) AddMover (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) AddMPLigandMover (class in pyrosetta.rosetta.protocols.membrane) AddMPLigandMoverCreator (class in pyrosetta.rosetta.protocols.membrane) AddOrDeleteMover (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) AddOrRemoveMatchCsts (class in pyrosetta.rosetta.protocols.enzdes) AddProperty (class in pyrosetta.rosetta.core.chemical) AddPyMOLObserver() (in module pyrosetta.rosetta.protocols.moves) AddPyMOLObserver_to_conformation() (in module pyrosetta.rosetta.protocols.moves) AddPyMOLObserver_to_energies() (in module pyrosetta.rosetta.protocols.moves) AddResidue() (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) AddResiduesRotamerSetOperation (class in pyrosetta.rosetta.core.pack.rotamer_set) adds_atom() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.RenameAtom method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.Set_AA method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) adds_atoms() (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) adds_properties() (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) adds_property() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.RenameAtom method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.Set_AA method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) addScoresForLoopParts() (in module pyrosetta.rosetta.protocols.loops) AddSegmentDataMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) AddStatus (class in pyrosetta.rosetta.protocols.optimize_weights) Adduct (class in pyrosetta.rosetta.core.chemical) adduct_name() (pyrosetta.rosetta.core.chemical.Adduct method) adducts() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) addVirtualResAsRoot() (in module pyrosetta.rosetta.core.pose) AddZincSiteConstraints (class in pyrosetta.rosetta.protocols.metal_interface) ADJ_LIST_MODE (class in pyrosetta.rosetta.protocols.cluster.calibur) AdjacentRemainingNodes() (in module pyrosetta.rosetta.protocols.toolbox) adjust_mm_to_length() (in module pyrosetta.rosetta.protocols.seeded_abinitio) adjust_relax_movemap() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) advance_euler_angles() (in module pyrosetta.rosetta.protocols.match) advance_to_next_pose_segment() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) affix_has_inherent_position() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) aggregate_function() (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) Ai() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) ala_constraint_over_strength() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) ala_constraint_under_strength() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) algorithm() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) align() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) align_and_output_to_silent_file() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) align_mainchain_atoms() (in module pyrosetta.rosetta.protocols.helical_bundle) align_mainchain_atoms_of_residue_range() (in module pyrosetta.rosetta.protocols.helical_bundle) align_model() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) align_motif_pose() (in module pyrosetta.rosetta.core.scoring.motif) align_motif_pose_break() (in module pyrosetta.rosetta.core.scoring.motif) align_motif_pose_by_one_frame() (in module pyrosetta.rosetta.core.scoring.motif) align_motif_pose_super() (in module pyrosetta.rosetta.core.scoring.motif) align_naive() (in module pyrosetta.rosetta.core.sequence) align_pose() (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) align_pose_and_add_rmsd_constraints() (in module pyrosetta.rosetta.protocols.stepwise.modeler.align) align_poses() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) align_poses_naive() (in module pyrosetta.rosetta.core.sequence) align_to_native() (in module pyrosetta.rosetta.protocols.antibody) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) align_virtual_atoms_in_carbohydrate_residue() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) alignaxis() (in module pyrosetta.rosetta.protocols.sic_dock) alignaxis_xform() (in module pyrosetta.rosetta.protocols.sic_dock) AlignByResidueSelectorMover (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) AlignChainMover (class in pyrosetta.rosetta.protocols.simple_moves) AlignedThreadOperation (class in pyrosetta.rosetta.protocols.task_operations) alignment() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) alignment_anchor_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) alignment_file() (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation method) alignment_from_pose() (in module pyrosetta.rosetta.core.sequence) alignment_id() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) alignment_into_pose() (in module pyrosetta.rosetta.core.sequence) alignment_probabilities() (in module pyrosetta.rosetta.protocols.medal) AlignmentAAFinder (class in pyrosetta.rosetta.protocols.evolution) AlignmentEnergy (class in pyrosetta.rosetta.protocols.rna) AlignmentGapInserter (class in pyrosetta.rosetta.protocols.evolution) alignments_from_cmd_line() (in module pyrosetta.rosetta.protocols.comparative_modeling) AlignMove (class in pyrosetta.rosetta.core.sequence) AlignOption (class in pyrosetta.rosetta.protocols.hybridization) AlignPoseToInvrotTreeMover (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) AlignResiduesMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) AlignRmsdTargetEvaluatorCreator (class in pyrosetta.rosetta.protocols.comparative_modeling) all_aligned() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) all_atom_center() (in module pyrosetta.rosetta.core.conformation) (in module pyrosetta.rosetta.core.pose) all_atom_rmsd() (in module pyrosetta.rosetta.core.scoring) all_atom_rmsd_nosuper() (in module pyrosetta.rosetta.core.scoring) all_bb_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) all_broker_files() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) all_cdr_fold_tree() (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) all_cdrs() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) all_energies_begin() (pyrosetta.rosetta.core.scoring.ScoreFunction method) all_energies_end() (pyrosetta.rosetta.core.scoring.ScoreFunction method) all_false_selection() (in module pyrosetta.rosetta.core.select.residue_selector) all_methods() (pyrosetta.rosetta.core.scoring.ScoreFunction method) all_pairs_shortest_paths() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Graph method) all_ref_poses() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) all_sc_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) all_scatom_rmsd_nosuper() (in module pyrosetta.rosetta.core.scoring) all_segments() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) all_target_res() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) all_true_selection() (in module pyrosetta.rosetta.core.select.residue_selector) ALLAA (class in pyrosetta.rosetta.core.pack.task) ALLAAwc (class in pyrosetta.rosetta.core.pack.task) ALLAAxc (class in pyrosetta.rosetta.core.pack.task) alllevel() (pyrosetta.rosetta.core.sequence.ABEGOManager method) allocate_matrix() (in module pyrosetta.rosetta.protocols.frag_picker.scores) allow_aa() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) allow_all_aas() (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) allow_base_pair_only_centroid_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) allow_bondangles() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) allow_bondlengths() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) allow_bulge_at_chainbreak() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) allow_claim() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) allow_design() (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) allow_design_around() (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation method) allow_dihedrals() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) allow_hbond() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) allow_noncanonical_aa() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) allow_rama_mismatches() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher method) allow_reading_cancelled_decoys() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) allow_rebuild_bulge_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) allow_repacking() (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) allow_syn_pyrimidine() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) allow_virtual_o2prime_hydrogens() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) allow_virtual_side_chains() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) allowed_closure_attempts() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) allowed_res_name3_at_position() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) allowed_res_types() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) allowed_res_types_pointers() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) allowed_residue_types() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) allowed_residue_types_begin() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) allowed_residue_types_end() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) AllowedSeqposForGeomCst (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) AllowPdbIdFilter (class in pyrosetta.rosetta.protocols.frag_picker) AllResiduesChanged (class in pyrosetta.rosetta.protocols.abinitio) (class in pyrosetta.rosetta.protocols.hybridization) allsc() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) ALPHA() (in module pyrosetta.rosetta.numeric.crick_equations) alpha() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) alpha_aform() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) alpha_deriv_func() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) alpha_func() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) alt_loc() (pyrosetta.rosetta.core.pose.PDBInfo method) alt_rot_matrix() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) alter_espGrid() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) alter_espGrid_with_bound_ligand() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) alter_rotamer_set() (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) alternative_decoys_out() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) AlterSpecDisruptionDriver (class in pyrosetta.rosetta.protocols.pmut_scan) AmberPeriodicFunc (class in pyrosetta.rosetta.core.scoring.func) AmbigCSScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) ambiguity() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) AmbiguousConstraint (class in pyrosetta.rosetta.core.scoring.constraints) AmbiguousConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) AmbiguousNMRConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) AmbiguousNMRDistanceConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) amoeba_type_lookup() (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) analytic_etable_derivatives() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) analytic_etable_evaluation() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) analytic_lk_derivatives() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) analytic_lk_energy() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) analytic_params_for_pair() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) Ancestor (class in pyrosetta.rosetta.core.chemical) Anchor (class in pyrosetta.rosetta.protocols.anchored_design) anchor_at_res1() (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) anchor_end() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) anchor_noise_constraints_setup() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) anchor_resnum() (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) anchor_start() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) anchored_loop() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) AnchoredGraftMover (class in pyrosetta.rosetta.protocols.grafting) AnchoredPerturbMover (class in pyrosetta.rosetta.protocols.anchored_design) AnchorMoversData (class in pyrosetta.rosetta.protocols.anchored_design) AND_combine() (in module pyrosetta.rosetta.core.select.residue_selector) and_extrachi_cutoff() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) and_linmem_ig() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) and_max_rotbump_energy() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) AndExpression (class in pyrosetta.rosetta.numeric.expression_parser) AndJumpSelector (class in pyrosetta.rosetta.core.select.jump_selector) AndResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) AndSelector (class in pyrosetta.rosetta.protocols.pose_selectors) ang_U1D2_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) ang_U2D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) angle() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) angle_degrees() (in module pyrosetta.rosetta.numeric) angle_degrees_double() (in module pyrosetta.rosetta.numeric) angle_disp() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) angle_distance() (in module pyrosetta.rosetta.core.scoring.motif) angle_exponent() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions method) angle_in_range() (in module pyrosetta.rosetta.basic) angle_max() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) angle_radians() (in module pyrosetta.rosetta.numeric) angle_radians_double() (in module pyrosetta.rosetta.numeric) angle_shift_factor() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions method) angle_threshold() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) AngleConstraint (class in pyrosetta.rosetta.core.scoring.constraints) AngleConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) AngleUnit (class in pyrosetta.rosetta.numeric.conversions) AngularMomentumQuantumNumber_strings() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) annotated_name() (pyrosetta.rosetta.core.conformation.Residue method) annotated_sequence() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) annotated_sequence_from_IUPAC_sequence() (pyrosetta.rosetta.core.io.NomenclatureManager method) annotated_sequence_from_modomics_oneletter_sequence() (pyrosetta.rosetta.core.io.NomenclatureManager method) annotated_to_oneletter_sequence() (in module pyrosetta.rosetta.core.pose) AnnotatedFragData (class in pyrosetta.rosetta.core.fragment) anomeric_position_from_code() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) Antibody (class in pyrosetta.rosetta.protocols.antibody_legacy) antibody_grafting_usable() (in module pyrosetta.rosetta.protocols.antibody.grafting) antibody_modeling_insert_ter() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) antibody_region_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) antibody_region_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) AntibodyCDRGrafter (class in pyrosetta.rosetta.protocols.antibody) AntibodyChain (class in pyrosetta.rosetta.protocols.antibody.grafting) AntibodyDatabaseManager (class in pyrosetta.rosetta.protocols.antibody) AntibodyDesignMover (class in pyrosetta.rosetta.protocols.antibody.design) AntibodyDesignProtocol (class in pyrosetta.rosetta.protocols.antibody.design) AntibodyDesignProtocolEnum (class in pyrosetta.rosetta.protocols.antibody.design) AntibodyEnumManager (class in pyrosetta.rosetta.protocols.antibody) AntibodyFeatures (class in pyrosetta.rosetta.protocols.antibody) AntibodyFeaturesCreator (class in pyrosetta.rosetta.protocols.antibody) AntibodyInfo (class in pyrosetta.rosetta.protocols.antibody) AntibodyNumberingConverterMover (class in pyrosetta.rosetta.protocols.antibody) AntibodyNumberingParser (class in pyrosetta.rosetta.protocols.antibody) AntibodyNumberingSchemeEnum (class in pyrosetta.rosetta.protocols.antibody) AntibodyRegionEnum (class in pyrosetta.rosetta.protocols.antibody) AntibodyRegionSelector (class in pyrosetta.rosetta.protocols.antibody.residue_selector) AntibodySeqDesignTFCreator (class in pyrosetta.rosetta.protocols.antibody.design) AntibodySequence (class in pyrosetta.rosetta.protocols.antibody.grafting) antigen_present() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) antiparallel() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) any_active_enmeths() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) any_exposed_dots() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) any_lr_residue_pair_energy() (pyrosetta.rosetta.core.scoring.ScoreFunction method) any_neighbors_for_residue() (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) any_unassigned() (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) any_upper_neighbors_for_residue() (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) any_vertex_state_unassigned() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) AnyOptionKey (class in pyrosetta.rosetta.utility.options) AnyVectorOptionKey (class in pyrosetta.rosetta.utility.options) APBSConfig (class in pyrosetta.rosetta.core.scoring) APBSResult (class in pyrosetta.rosetta.core.scoring) APBSWrapper (class in pyrosetta.rosetta.core.scoring) APCluster (class in pyrosetta.rosetta.protocols.cluster) APOLA (class in pyrosetta.rosetta.core.pack.task) APOLAR (class in pyrosetta.rosetta.core.pack.task) APolarHydrogenFilter (class in pyrosetta.rosetta.core.chemical) append() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) append_aa_composition_setup_files() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) append_atom() (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) append_atoms() (pyrosetta.rosetta.core.io.ResidueInformation method) append_attributes() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator method) append_choices() (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) append_comparer_attributes() (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) append_fold_tree_to_file() (in module pyrosetta.rosetta.protocols.backrub) append_fragment() (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) append_hbond() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) append_index() (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) append_mg_bound_water() (in module pyrosetta.rosetta.protocols.magnesium) append_model() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) append_name_and_attributes_to_complex_type() (in module pyrosetta.rosetta.utility.tag) append_netcharge_setup_files() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) append_new_chain_from_template_segment() (in module pyrosetta.rosetta.protocols.denovo_design.components) append_new_residues() (in module pyrosetta.rosetta.protocols.denovo_design.components) append_op() (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) append_particle() (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) append_particles() (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) append_polymer_residue_after_seqpos() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) append_pose_by_jump() (pyrosetta.rosetta.core.pose.Pose method) append_pose_to_pose() (in module pyrosetta.rosetta.core.pose) append_pose_to_pose_keep_fold_tree() (in module pyrosetta.rosetta.protocols.fold_from_loops.utils) append_pose_with_glycan_residues() (in module pyrosetta.rosetta.core.pose) append_protocol_attributes() (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) append_reporter_attributes() (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) append_required_name_and_attributes_to_complex_type() (in module pyrosetta.rosetta.utility.tag) append_res() (pyrosetta.rosetta.core.pose.PDBInfo method) append_residue() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.kinematics.FoldTree method) append_residue_by_atoms() (pyrosetta.rosetta.core.pose.Pose method) append_residue_by_bond() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) append_residue_by_chemical_bond() (pyrosetta.rosetta.core.kinematics.FoldTree method) append_residue_by_jump() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) append_residue_to_sfr() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) append_residues_from_template_segment() (in module pyrosetta.rosetta.protocols.denovo_design.components) append_rotamer_operation() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) append_rotamerset_operation() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) append_schema_attributes() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) append_segments() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) append_single_far_away_water() (in module pyrosetta.rosetta.protocols.hydrate) append_subelement_and_attributes_for_parse_loops_from_tag() (in module pyrosetta.rosetta.protocols.loop_modeling.utilities) append_subelement_for_parse_movemap_factory_legacy() (in module pyrosetta.rosetta.protocols.rosetta_scripts) append_subpose_to_pose() (in module pyrosetta.rosetta.core.pose) append_to_additional_string_output() (pyrosetta.rosetta.core.io.StructFileRep method) append_virtual_residue_to_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) AppendMainchainAtom (class in pyrosetta.rosetta.core.chemical) AppendResidueRotamerSet (class in pyrosetta.rosetta.core.pack.task.operation) AppendRotamer (class in pyrosetta.rosetta.core.pack.task.operation) AppendRotamerSet (class in pyrosetta.rosetta.core.pack.task.operation) applicable() (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) applies_to() (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) applies_to_placeholder() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.RenameAtom method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.Set_AA method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) apply() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.RenameAtom method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.Set_AA method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.scoring.TMscoreStore method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.TotalEnergyMetric method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.Revert method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) apply_A_LH_foldtree() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) apply_adducts_to_residue() (in module pyrosetta.rosetta.core.chemical) apply_Aform_torsions() (in module pyrosetta.rosetta.core.pose.rna) apply_after_jump_change() (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) apply_and_return_jump() (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) apply_and_to_subset() (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) apply_at_all_positions() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) apply_at_domain() (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) apply_best_scoring_fragdata() (in module pyrosetta.rosetta.core.fragment) apply_body() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) apply_chi_cst() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) apply_closure() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) apply_const() (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) apply_current_pose_segment() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) apply_disulfides() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) apply_dofs() (in module pyrosetta.rosetta.core.pose.copydofs) apply_fragment() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) apply_from_template_pose() (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) apply_full_to_sub_mapping() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) apply_ideal_c2endo_sugar_coords() (in module pyrosetta.rosetta.core.pose.rna) apply_if_reasonable() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution method) apply_multi() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) apply_non_main_chain_sugar_coords() (in module pyrosetta.rosetta.core.pose.rna) apply_nucleoside_torsion_Aform() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) apply_or_to_subset() (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) apply_patch_from_file() (pyrosetta.rosetta.core.scoring.ScoreFunction method) apply_protonated_H1_adenosine_variant_type() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) apply_pucker() (in module pyrosetta.rosetta.core.pose.rna) apply_random_fragment() (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) apply_random_nucleoside_torsion() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) apply_random_suite_torsion() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) apply_repeat() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) apply_rotate() (in module pyrosetta.rosetta.protocols.ligand_docking) apply_sequence_mapping() (in module pyrosetta.rosetta.protocols.loops) (pyrosetta.rosetta.core.kinematics.FoldTree method) apply_set_weights() (in module pyrosetta.rosetta.core.scoring) apply_ss() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) apply_sub_to_full_mapping() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) apply_suite_torsion_Aform() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) apply_superposition_transform() (in module pyrosetta.rosetta.protocols.toolbox) apply_superposition_transform_to_jump() (in module pyrosetta.rosetta.protocols.toolbox) apply_symm_gly_corrections() (in module pyrosetta.rosetta.core.chemical) apply_to_cdr() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) apply_to_pose() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) apply_to_rotpack() (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) apply_transform() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) apply_transform_Rx_plus_v() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) apply_transformation() (in module pyrosetta.rosetta.protocols.forge.methods) (in module pyrosetta.rosetta.protocols.hybridization) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) apply_transformation_norecompute() (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) apply_virtual_rna_residue_variant_type() (in module pyrosetta.rosetta.core.pose.rna) ApplyRandomStoredRBConf (class in pyrosetta.rosetta.protocols.enzdes) applyRotation() (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) applySpin() (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) applyTransformation() (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) applyTranslation() (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) architect() (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) architect_group_name() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) architect_name() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) ArchiveManager (class in pyrosetta.rosetta.protocols.jd2.archive) are_colliding() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) are_coplanar() (in module pyrosetta.rosetta.numeric.geometry) are_selections_equal() (in module pyrosetta.rosetta.core.select.residue_selector) are_seqs_different() (in module pyrosetta.rosetta.protocols.vip) are_they_neighbors() (pyrosetta.rosetta.core.scoring.ScoreFunction method) arg_min() (in module pyrosetta.rosetta.utility) argrot_dna_dis2() (in module pyrosetta.rosetta.protocols.dna) ArithmeticASTNode (class in pyrosetta.rosetta.numeric.expression_parser) ArithmeticASTValue (class in pyrosetta.rosetta.numeric.expression_parser) Armijo() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) ArmijoLineMinimization (class in pyrosetta.rosetta.core.optimization) AROMATIC (class in pyrosetta.rosetta.core.pack.task) AromaticAtomFilter (class in pyrosetta.rosetta.core.chemical) aromaticity() (pyrosetta.rosetta.core.chemical.Bond method) array_pool() (pyrosetta.rosetta.core.scoring.EnergyGraph method) asp_corrections() (in module pyrosetta.rosetta.protocols.make_rot_lib) aspartimide_penalty_value() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) assemble_remark_line() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) assemble_remark_lines() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) Assembly (class in pyrosetta.rosetta.protocols.legacy_sewing) AssemblyFactory (class in pyrosetta.rosetta.protocols.legacy_sewing) assert_phosphate_nomenclature_matches_mini() (in module pyrosetta.rosetta.core.pose.rna) assign() (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.basic.ExecutionResult method) (pyrosetta.rosetta.basic.Report method) (pyrosetta.rosetta.basic.Reporter method) (pyrosetta.rosetta.basic.datacache.CacheableData method) (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringIntegerMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.ConstDataMap method) (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceStream method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream method) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream method) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter method) (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter method) (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.ElementSet method) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RealFilter method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.RenameAtom method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResConnID method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle method) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent method) (pyrosetta.rosetta.core.chemical.Selector_AA method) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG method) (pyrosetta.rosetta.core.chemical.Selector_HAS_ATOMS method) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_NAME1 method) (pyrosetta.rosetta.core.chemical.Selector_NAME3 method) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY method) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION method) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.Set_AA method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) (pyrosetta.rosetta.core.chemical.rings.RingConformer method) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter method) (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.conformation.Atom method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo method) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent method) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent method) (pyrosetta.rosetta.core.conformation.signals.XYZEvent method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.enzymes.EnzymeData method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragmentSetLoader method) (pyrosetta.rosetta.core.fragment.FragmentSetLoaderCreator method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore method) (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.id.NamedStubID method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator method) (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepSequence method) (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) (pyrosetta.rosetta.core.import_pose.libraries.RNA_JumpLibrary method) (pyrosetta.rosetta.core.io.AtomInformation method) (pyrosetta.rosetta.core.io.CisPeptideInformation method) (pyrosetta.rosetta.core.io.HELIXInformation method) (pyrosetta.rosetta.core.io.HeaderInformation method) (pyrosetta.rosetta.core.io.LinkInformation method) (pyrosetta.rosetta.core.io.ModifiedResidueInformation method) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.io.SHEETInformation method) (pyrosetta.rosetta.core.io.SSBondInformation method) (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder method) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.rna.RNA_DataReader method) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStructCreator method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) (pyrosetta.rosetta.core.kinematics.Stub method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.CartesianMinimizer method) (pyrosetta.rosetta.core.optimization.ConvergenceTest method) (pyrosetta.rosetta.core.optimization.Particle method) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphContainer method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AROMATIC method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.CHARGED method) (pyrosetta.rosetta.core.pack.task.EMPTY method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NC method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.PIKRNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PROPERTY method) (pyrosetta.rosetta.core.pack.task.RESET method) (pyrosetta.rosetta.core.pack.task.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.pose.rna.BasePairStep method) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) (pyrosetta.rosetta.core.pose.rna.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.core.pose.signals.ConformationEvent method) (pyrosetta.rosetta.core.pose.signals.DestructionEvent method) (pyrosetta.rosetta.core.pose.signals.EnergyEvent method) (pyrosetta.rosetta.core.pose.signals.GeneralEvent method) (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.core.scoring.APBSConfig method) (pyrosetta.rosetta.core.scoring.APBSResult method) (pyrosetta.rosetta.core.scoring.APBSWrapper method) (pyrosetta.rosetta.core.scoring.AtomNeighbor method) (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.DerivVectorPair method) (pyrosetta.rosetta.core.scoring.DipolarCoupling method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.GenericBondedPotential method) (pyrosetta.rosetta.core.scoring.Hairpin method) (pyrosetta.rosetta.core.scoring.Helices method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.PQR method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.Predicate method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.ResRangePredicate method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) (pyrosetta.rosetta.core.scoring.Strands method) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.dssp.Dssp method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.func.XYZ_Func method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup method) (pyrosetta.rosetta.core.scoring.packing.HolesResult method) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.scoring.sc._RESULTS method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelector method) (pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.core.sequence.Line method) (pyrosetta.rosetta.core.sequence.SSManager method) (pyrosetta.rosetta.core.sequence.SequenceCreator method) (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter method) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor method) (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.Expression method) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression method) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree method) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceData method) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.TotalEnergyMetric method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.cluster.APCluster method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.contact_map.Contact method) (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) (pyrosetta.rosetta.protocols.cryst.CheshireCell method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.dna.DnaDesignDef method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions method) (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringProtocol method) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator method) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator method) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator method) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.filters.FilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMoverCreator method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.Interval method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination method) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition method) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent method) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore method) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector method) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector method) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct method) (pyrosetta.rosetta.protocols.hbnet.HBondResStruct method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.Job method) (pyrosetta.rosetta.protocols.jd3.JobOutputIndex method) (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.JobResult method) (pyrosetta.rosetta.protocols.jd3.JobSummary method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) (pyrosetta.rosetta.protocols.jd3.output.OutputSpecification method) (pyrosetta.rosetta.protocols.jd3.output.ResultOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) (pyrosetta.rosetta.protocols.jumping.SameStrand method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.Basis method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalRequirementCreator method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LocalInserter method) (pyrosetta.rosetta.protocols.loophash.LocalInserter_SimpleMin method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.Loop_lt method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.LoopsFileIO method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator method) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader method) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM method) (pyrosetta.rosetta.protocols.match.BfactorMPM method) (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.MatchPositionModifier method) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM method) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM method) (pyrosetta.rosetta.protocols.match.TaskOperationMPM method) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.ResHasher method) (pyrosetta.rosetta.protocols.mean_field.ResPred method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraintCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraintCreator method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator method) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.GeometricFunc method) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoverCreator method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.ResId method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.NoFailDataMap method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.PoseForPoseID method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) (pyrosetta.rosetta.protocols.neighbor.Neighborhood method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.Chunk method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.Policy method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy method) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator method) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader method) (pyrosetta.rosetta.protocols.parser.DataLoader method) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DatabaseSessionLoader method) (pyrosetta.rosetta.protocols.parser.FragSetLoader method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) (pyrosetta.rosetta.protocols.parser.ResLvlTaskOperationLoader method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader method) (pyrosetta.rosetta.protocols.parser.SimpleMetricLoader method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator method) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt method) (pyrosetta.rosetta.protocols.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborsByDistanceCalculator method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) (pyrosetta.rosetta.protocols.protein_interface_design.Revert method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.NCSResMapping method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation method) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KClusterData method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnitList method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs method) (pyrosetta.rosetta.utility.CSI_Sequence method) (pyrosetta.rosetta.utility.excn.BadInput method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.EdgeListIterator method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.io.FileContentsMap method) (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.OptionCollection method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) (pyrosetta.rosetta.utility.py.Base method) (pyrosetta.rosetta.utility.py.PyExitCallback method) (pyrosetta.rosetta.utility.py.Value method) (pyrosetta.rosetta.utility.recent_history_queue method) (pyrosetta.rosetta.utility.signals.Link method) (pyrosetta.rosetta.utility.subset_mapping method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaType method)

assign_abase_derivs() (in module pyrosetta.rosetta.core.scoring.hbonds) assign_all_amoeba_types() (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) assign_best_rotamer() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) assign_energy() (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) assign_gasteiger_atom_types() (in module pyrosetta.rosetta.core.chemical.gasteiger) assign_group_for_match() (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) assign_if() (pyrosetta.rosetta.ObjexxFCL.Dimension method) assign_if_bigger() (pyrosetta.rosetta.ObjexxFCL.Dimension method) assign_if_bigger_nic() (pyrosetta.rosetta.ObjexxFCL.Dimension method) assign_if_half() (pyrosetta.rosetta.ObjexxFCL.Dimension method) assign_if_half_nic() (pyrosetta.rosetta.ObjexxFCL.Dimension method) assign_if_nic() (pyrosetta.rosetta.ObjexxFCL.Dimension method) assign_internal_coordinates() (pyrosetta.rosetta.core.chemical.ResidueType method) assign_neighbor_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) assign_no_notify() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) assign_pucker() (in module pyrosetta.rosetta.core.pose.rna) assign_random_rotamer() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) assign_random_rotamer_with_bias() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) assign_residue_amoeba_type() (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) assign_ss_dssp() (in module pyrosetta.rosetta.protocols.jumping) assign_state() (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) assign_type_data() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) assign_value_of() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) assignments() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) ast_string() (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter method) ASTPrinter (class in pyrosetta.rosetta.numeric.expression_parser) ASTVisitor (class in pyrosetta.rosetta.numeric.expression_parser) AsymFoldandDockMoveRbJumpMover (class in pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock) AsymFoldandDockRbTrialMover (class in pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock) asymmetric_dof() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) asymmetrize_scorefunction() (in module pyrosetta.rosetta.core.scoring.symmetry) at() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) at_end() (pyrosetta.rosetta.protocols.match.VoxelSetIterator method) at_inds() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) atmid() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) atmname_using() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) Atom (class in pyrosetta.rosetta.core.chemical) (class in pyrosetta.rosetta.core.conformation) (class in pyrosetta.rosetta.core.kinematics.tree) atom() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.id.NamedStubID method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) atom1() (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) atom2() (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) atom3() (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) Atom_ (class in pyrosetta.rosetta.core.kinematics.tree) atom_aliases() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_base() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) atom_begin() (pyrosetta.rosetta.core.conformation.Residue method) atom_being_shadowed() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_charge() (pyrosetta.rosetta.core.chemical.Adduct method) atom_controlled_by_any_chi() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) atom_data() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) atom_depends_on_connection() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_depends_on_lower() (pyrosetta.rosetta.core.conformation.Residue method) atom_depends_on_lower_polymeric_connection() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_depends_on_polymeric_connection() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_depends_on_upper() (pyrosetta.rosetta.core.conformation.Residue method) atom_depends_on_upper_polymeric_connection() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_derivatives() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) atom_distance() (in module pyrosetta.rosetta.protocols.protein_interface_design.filters) (in module pyrosetta.rosetta.protocols.simple_filters) atom_dont_do_update() (pyrosetta.rosetta.core.kinematics.AtomTree method) atom_end() (pyrosetta.rosetta.core.conformation.Residue method) atom_forms_residue_connection() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_geom_rpes() (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) atom_gets_derivatives() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) atom_has_nonchi_coordinate() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) atom_has_orbital() (pyrosetta.rosetta.core.chemical.AtomType method) atom_hbonds() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) atom_hbonds_all() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) atom_id() (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) atom_id_mapper() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) atom_id_to_named_atom_id() (in module pyrosetta.rosetta.core.conformation) (in module pyrosetta.rosetta.core.pose) atom_index() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) atom_inds_for_restype() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) atom_inds_for_restype_begin() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) atom_inds_for_restype_end() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) atom_is_backbone() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) atom_is_backbone_norefold() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) atom_is_chitip() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) atom_is_hydratable() (in module pyrosetta.rosetta.protocols.hydrate) atom_is_hydrogen() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) atom_is_on_path_from_root() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) atom_is_phosphate() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) atom_is_polar_hydrogen() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) atom_is_sidechain() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_is_virtual() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) atom_iterators() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_level_domain_map() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) atom_map_from_score_result() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) atom_map_valid_size() (in module pyrosetta.rosetta.protocols.hybridization) atom_mode() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) atom_name() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) atom_name1() (pyrosetta.rosetta.core.import_pose.libraries.RNA_PairingTemplate method) atom_name2() (pyrosetta.rosetta.core.import_pose.libraries.RNA_PairingTemplate method) atom_names_list() (pyrosetta.rosetta.core.pose.MiniPose method) atom_neighbors() (pyrosetta.rosetta.core.scoring.NeighborList method) atom_numbers_for_mg_calculation() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) atom_numbers_for_vdw_calculation() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) atom_overlap_is_exposed() (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) atom_overlaps_voxel() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) atom_pair_constraint_weight() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) atom_pair_energy_v() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) atom_pair_lk_energy_and_deriv_v() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) atom_pair_lk_energy_and_deriv_v_efficient() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) atom_radius() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) atom_score() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) atom_set() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) atom_specific_rms() (in module pyrosetta.rosetta.protocols.motifs) atom_square_deviation() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) atom_tree() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) atom_tree_dfunc() (in module pyrosetta.rosetta.core.optimization) (in module pyrosetta.rosetta.core.optimization.symmetry) atom_tree_get_atompairE_deriv() (in module pyrosetta.rosetta.core.optimization) (in module pyrosetta.rosetta.core.optimization.symmetry) atom_type() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) atom_type_index() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.conformation.Residue method) atom_type_name() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomType method) atom_type_set() (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.conformation.Residue method) atom_type_set_ptr() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_vdw_atom_type_set_name() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) atom_vertex() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_z_position() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) AtomAngleSecMatchRPE (class in pyrosetta.rosetta.protocols.match.downstream) AtomAtomPairFeaturesCreator (class in pyrosetta.rosetta.protocols.features) AtomBasedConstraintsScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) AtomDihedralSecMatchRPE (class in pyrosetta.rosetta.protocols.match.downstream) AtomDistanceSecMatchRPE (class in pyrosetta.rosetta.protocols.match.downstream) AtomGeometrySecMatchRPE (class in pyrosetta.rosetta.protocols.match.downstream) atomic_charge() (pyrosetta.rosetta.core.conformation.Residue method) atomic_interaction_cutoff() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) atomic_radius() (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) AtomicContactFilter (class in pyrosetta.rosetta.protocols.simple_filters) AtomicDistanceFilter (class in pyrosetta.rosetta.protocols.simple_filters) AtomICoor (class in pyrosetta.rosetta.core.chemical) AtomicOrbitalTypes_strings() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) AtomID (class in pyrosetta.rosetta.core.id) AtomInformation (class in pyrosetta.rosetta.core.io) AtomInResidueAtomInResiduePairFeaturesCreator (class in pyrosetta.rosetta.protocols.features) atomitem (class in pyrosetta.rosetta.core.scoring.rna.chemical_shift) AtomLevelDomainMap (class in pyrosetta.rosetta.core.pose.toolbox) AtomLevelHBondEdge (class in pyrosetta.rosetta.core.scoring.hbonds.graph) AtomLevelHBondNode (class in pyrosetta.rosetta.core.scoring.hbonds.graph) atomname() (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) AtomNeighbor (class in pyrosetta.rosetta.core.scoring) atomno() (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.scoring.AtomNeighbor method) AtomPairConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) AtomPairConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) AtomPairConstraintsData (class in pyrosetta.rosetta.protocols.frag_picker.scores) AtomPairConstraintsScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) AtomPairData (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) AtomProperties (class in pyrosetta.rosetta.core.chemical) AtomPropertiesManager (class in pyrosetta.rosetta.core.chemical) AtomProperty (class in pyrosetta.rosetta.core.chemical) atoms() (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) atoms_are_bonded() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) atoms_begin() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) atoms_end() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) atoms_interact() (in module pyrosetta.rosetta.core.scoring.methods) atoms_last_controlled_by_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) atoms_per_residue() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) atoms_with_orb_index() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) atoms_within_one_bond_of_a_residue_connection() (pyrosetta.rosetta.core.chemical.ResidueType method) atoms_within_two_bonds_of_a_residue_connection() (pyrosetta.rosetta.core.chemical.ResidueType method) AtomTree (class in pyrosetta.rosetta.core.kinematics) AtomTreeCollection (class in pyrosetta.rosetta.core.pack.scmin) AtomTreeDiff (class in pyrosetta.rosetta.core.import_pose.atom_tree_diffs) AtomTreeDiffJobDistributor (class in pyrosetta.rosetta.protocols.jobdist) AtomTreeDiffJobInputter (class in pyrosetta.rosetta.protocols.jd2) AtomTreeDiffJobOutputter (class in pyrosetta.rosetta.protocols.jd2) AtomTreeMinimizer (class in pyrosetta.rosetta.core.optimization) AtomTreeMultifunc (class in pyrosetta.rosetta.core.optimization) AtomType (class in pyrosetta.rosetta.core.chemical) AtomTypeSet (class in pyrosetta.rosetta.core.chemical) AtomTypesFeaturesCreator (class in pyrosetta.rosetta.protocols.features) AtomWithDOFChange (class in pyrosetta.rosetta.core.kinematics) atr_rep_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) atr_rep_screen_for_docking() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) atr_weight() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) attach() (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) attach_boinc_ghost_observer() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) attach_impl() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) attach_n_and_c_unfolded_poses_to_pose() (in module pyrosetta.rosetta.protocols.fold_from_loops.utils) attach_observer() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) attach_secondary_structure_pools() (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) attach_to() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) attach_to_conformation() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) attach_unfolded_pose_to_pose_c_term() (in module pyrosetta.rosetta.protocols.fold_from_loops.utils) attach_unfolded_pose_to_pose_n_term() (in module pyrosetta.rosetta.protocols.fold_from_loops.utils) attached_H_begin() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) attached_H_end() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) attached_res() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) Attachment (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) attachment_type() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) attachment_type_from_string() (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) attachments() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) AttachmentType (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) attempt_insert() (pyrosetta.rosetta.protocols.mean_field.ResHashMap method) attribute_w_default() (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) attribute_w_name_in_attribute_list() (in module pyrosetta.rosetta.utility.tag) attributes() (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) attributes_for_get_ab_design_global_scorefxn() (in module pyrosetta.rosetta.protocols.antibody.design) attributes_for_get_ab_design_min_scorefxn() (in module pyrosetta.rosetta.protocols.antibody.design) attributes_for_get_cdr_bool_from_tag() (in module pyrosetta.rosetta.protocols.antibody) attributes_for_get_resnum_selector() (in module pyrosetta.rosetta.core.pose) attributes_for_get_resnum_string() (in module pyrosetta.rosetta.core.pose) attributes_for_get_score_function_name() (in module pyrosetta.rosetta.core.scoring) attributes_for_get_score_function_name_w_description() (in module pyrosetta.rosetta.core.scoring) attributes_for_load_loop_definitions() (in module pyrosetta.rosetta.protocols.loops.loops_definers) attributes_for_parse_center_normal_from_tag() (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) attributes_for_parse_constraint_generators() (in module pyrosetta.rosetta.protocols.constraint_generator) attributes_for_parse_database_connection() (in module pyrosetta.rosetta.basic.database) attributes_for_parse_database_session() (in module pyrosetta.rosetta.protocols.rosetta_scripts) attributes_for_parse_grid_set_from_tag() (in module pyrosetta.rosetta.protocols.qsar.scoring_grid) attributes_for_parse_jump_selector() (in module pyrosetta.rosetta.core.select.jump_selector) attributes_for_parse_jump_selector_default_option_name() (in module pyrosetta.rosetta.core.select.jump_selector) attributes_for_parse_jump_selector_when_required() (in module pyrosetta.rosetta.core.select.jump_selector) attributes_for_parse_movemap_factory() (in module pyrosetta.rosetta.core.select.movemap) attributes_for_parse_movemap_factory_default_attr_name() (in module pyrosetta.rosetta.core.select.movemap) attributes_for_parse_movemap_factory_when_required() (in module pyrosetta.rosetta.core.select.movemap) attributes_for_parse_movemap_factory_when_required_default_name() (in module pyrosetta.rosetta.core.select.movemap) attributes_for_parse_my_tag() (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) attributes_for_parse_optional_grid_set_from_tag() (in module pyrosetta.rosetta.protocols.qsar.scoring_grid) attributes_for_parse_residue_level_operations() (in module pyrosetta.rosetta.core.pack.task.operation) attributes_for_parse_residue_selector() (in module pyrosetta.rosetta.core.select.residue_selector) (in module pyrosetta.rosetta.protocols.rosetta_scripts) attributes_for_parse_residue_selector_default_option_name() (in module pyrosetta.rosetta.core.select.residue_selector) attributes_for_parse_residue_selector_logic_string() (in module pyrosetta.rosetta.core.select.residue_selector) attributes_for_parse_residue_selector_when_required() (in module pyrosetta.rosetta.core.select.residue_selector) attributes_for_parse_resnum() (in module pyrosetta.rosetta.core.pose) attributes_for_parse_score_function() (in module pyrosetta.rosetta.core.scoring) attributes_for_parse_score_function_w_description() (in module pyrosetta.rosetta.core.scoring) attributes_for_parse_score_function_w_description_when_required() (in module pyrosetta.rosetta.core.scoring) attributes_for_parse_task_operations() (in module pyrosetta.rosetta.core.pack.task) attributes_for_parse_task_operations_w_factory() (in module pyrosetta.rosetta.core.pack.task) attributes_for_parse_xyz_vector() (in module pyrosetta.rosetta.protocols.rosetta_scripts) attributes_for_remodel_constraint_generator() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) attributes_for_saved_reference_pose() (in module pyrosetta.rosetta.protocols.rosetta_scripts) attributes_for_saved_reference_pose_w_description() (in module pyrosetta.rosetta.protocols.rosetta_scripts) attributes_for_set_scorefxn_from_tag() (in module pyrosetta.rosetta.protocols.loop_modeling.utilities) attributes_for_set_task_factory_from_tag() (in module pyrosetta.rosetta.protocols.loop_modeling.utilities) attributes_for_tempering_base() (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) attributes_for_trajectory_recorder() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) AUTO (class in pyrosetta.rosetta.core.pack.task) auto_choose_cutpoint() (pyrosetta.rosetta.protocols.loops.Loop method) auto_choose_cutpoints() (pyrosetta.rosetta.protocols.loops.Loops method) auto_detect_glycan_connections() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) auto_detect_symmetry() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) auto_setup_all_metal_bonds() (in module pyrosetta.rosetta.core.util) auto_setup_all_metal_constraints() (in module pyrosetta.rosetta.core.util) auto_trim_floppy_termini() (in module pyrosetta.rosetta.protocols.sic_dock) autodetermine_chi_bonds() (pyrosetta.rosetta.core.chemical.ResidueType method) autoexpanding_pocket_eval() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) autogenerate_constseq_frags() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) autogenerate_design_frags() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) autogenerate_frags() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) automatic_distance_cutoff() (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) AutomaticSheetConstraintGenerator (class in pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator) automorphic_rmsd() (in module pyrosetta.rosetta.core.scoring) AutomorphismIterator (class in pyrosetta.rosetta.core.chemical) available_AAs_file() (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) available_resource_loaders() (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) average_antiparallel_embeddings() (in module pyrosetta.rosetta.protocols.membrane) average_embeddings() (in module pyrosetta.rosetta.protocols.membrane) average_residue_hASA() (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) average_score() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) average_shortest_path_length() (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) avg_cluster_cen_dist() (in module pyrosetta.rosetta.protocols.make_rot_lib) avoid_negative_zero() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) AxEqDesignation (class in pyrosetta.rosetta.core.chemical.rings) axis() (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method)

B

B() (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) b1() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) b1_b2_Ktheta() (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) b1_b2_theta0() (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) b1_bond_angle_A() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b1_bond_angle_B() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b1_bond_angle_C() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b1_torsion_offset_A() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b1_torsion_offset_B() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b1_torsion_offset_C() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b2() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) b2_bond_angle_A() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b2_bond_angle_B() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b2_bond_angle_C() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b2_torsion_offset_A() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b2_torsion_offset_B() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b2_torsion_offset_C() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) bab_motif() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) bab_motifs() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) back() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) backbone() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) backbone_aa() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) backbone_backbone_energy() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) backbone_burial() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) backbone_exposed() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) backbone_mover_complex_type_namer() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) backbone_only() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) backbone_sidechain_energy() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) backbone_stub_match() (in module pyrosetta.rosetta.protocols.motifs) BackboneGridSamplerHelper (class in pyrosetta.rosetta.protocols.helical_bundle) BackboneMover (class in pyrosetta.rosetta.protocols.simple_moves) BackboneStubConstraint (class in pyrosetta.rosetta.core.scoring.constraints) BackboneStubLinearConstraint (class in pyrosetta.rosetta.core.scoring.constraints) backrub_cdrs() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) backrub_rotation_angles() (in module pyrosetta.rosetta.protocols.backrub) backrub_rotation_constants() (in module pyrosetta.rosetta.protocols.backrub) BackrubMover (class in pyrosetta.rosetta.protocols.backrub) BackrubSegment (class in pyrosetta.rosetta.protocols.backrub) bad() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) BadInput (class in pyrosetta.rosetta.utility.excn) BalancedKicMover (class in pyrosetta.rosetta.protocols.kinematic_closure) BANGLE_MIN() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) BANGLE_SD() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) bare_name() (pyrosetta.rosetta.utility.file.FileName method) Base (class in pyrosetta.rosetta.utility.py) base() (pyrosetta.rosetta.utility.file.FileName method) base5index2symbolString() (pyrosetta.rosetta.core.sequence.ABEGOManager method) base_analogue() (pyrosetta.rosetta.core.chemical.ResidueType method) base_atoms_square_deviation() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) base_axis_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) base_backbone_distance_cutoff() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) base_backbone_rho_cutoff() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) base_backbone_z_cutoff() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) base_centroids() (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) base_geometry_height_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) base_geometry_orientation_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) base_name() (in module pyrosetta.rosetta.protocols.vip) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) base_native_bonus() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) base_pair_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) base_pair_list() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) base_pair_moving() (in module pyrosetta.rosetta.core.pose.rna) base_pair_step_moving() (in module pyrosetta.rosetta.core.pose.rna) base_residue_types() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) base_stack_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) base_stack_axis_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) base_stack_list() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) base_stagger_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) base_stubs() (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) base_type() (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) BaseArchiveManager (class in pyrosetta.rosetta.protocols.jd2.archive) BaseDoubletOrientation (class in pyrosetta.rosetta.core.chemical.rna) BaseEdge (class in pyrosetta.rosetta.core.chemical.rna) BaseJobDistributor (class in pyrosetta.rosetta.protocols.jobdist) BaseJumpSetup (class in pyrosetta.rosetta.protocols.jumping) baseline_checkpointing_filename() (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) basepair_axis_stagger_scaling() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) BasePairConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) BasePairStep (class in pyrosetta.rosetta.core.pose.rna) BasePairStepLibrary (class in pyrosetta.rosetta.core.import_pose.libraries) BasePairStepSequence (class in pyrosetta.rosetta.core.import_pose.libraries) BasePairType (class in pyrosetta.rosetta.core.import_pose.libraries) BasePartner (class in pyrosetta.rosetta.core.scoring.dna) basestack_axis_scaling() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) BaseStackWhichSide (class in pyrosetta.rosetta.core.chemical.rna) BaseTabooPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) basic_idealize() (in module pyrosetta.rosetta.protocols.idealize) BasicCDRClusterSet (class in pyrosetta.rosetta.protocols.antibody.clusters) BasicDataCache (class in pyrosetta.rosetta.basic.datacache) BasicJob (class in pyrosetta.rosetta.protocols.jobdist) Basis (class in pyrosetta.rosetta.protocols.legacy_sewing) basis_pair() (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) Batch (class in pyrosetta.rosetta.protocols.jd2.archive) batch() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) batch_get_xyz() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) batch_set_xyz() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.pose.Pose method) batches() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) BatchJobInputter (class in pyrosetta.rosetta.protocols.jd2) bb() (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) bb_bb() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) bb_boltz_probs() (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) bb_boltz_probs_per_aa() (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) bb_independent_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) bb_pair_score() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) BB_Pos (class in pyrosetta.rosetta.core.scoring) (class in pyrosetta.rosetta.protocols.fldsgn.topology) bb_pos() (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) bb_rmsd() (in module pyrosetta.rosetta.core.scoring) bb_rmsd_including_O() (in module pyrosetta.rosetta.core.scoring) bbdep_bond_devs() (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) bbdep_bond_params() (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) BBDihedralSampler (class in pyrosetta.rosetta.protocols.simple_moves.bb_sampler) BBDihedralSamplerBase (class in pyrosetta.rosetta.protocols.simple_moves.bb_sampler) BBDihedralSamplerMover (class in pyrosetta.rosetta.protocols.simple_moves) BBdisplayState (class in pyrosetta.rosetta.protocols.viewer.graphics_states_param) BBG8T3AMover (class in pyrosetta.rosetta.protocols.simple_moves) BBGaussianMover (class in pyrosetta.rosetta.protocols.simple_moves) bbnbrs() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) bbpos_is_set() (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) BBSampleType (class in pyrosetta.rosetta.protocols.simple_moves.bb_sampler) bbtorsion_srfd() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) be_lenient() (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) been_accessed() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) begin() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) begin1() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) begin_const() (pyrosetta.rosetta.core.io.raw_data.RawFileData method) begin_critical_section() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) begin_receptor_partner_pair() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) begin_structure() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) being_designed() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) being_packed() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) bend() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) bend_level() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) bessel_roots() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) best_bbcst_residues() (in module pyrosetta.rosetta.protocols.protein_interface_design) best_cutpoint() (in module pyrosetta.rosetta.protocols.protein_interface_design) best_rotamer_energy() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) BestHotspotCstMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) BestTotalScoreSelector (class in pyrosetta.rosetta.protocols.frag_picker) beta() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.CSA method) beta_aform() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) BetaAlphaBetaMotifSet (class in pyrosetta.rosetta.protocols.fldsgn.topology) BetaSheetArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) BetaTurnDetectionFeaturesCreator (class in pyrosetta.rosetta.protocols.features) bF() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) BFactor (class in pyrosetta.rosetta.protocols.frag_picker.scores) bfactor() (pyrosetta.rosetta.core.pose.PDBInfo method) BfactorFittingMover (class in pyrosetta.rosetta.protocols.electron_density) BfactorMPM (class in pyrosetta.rosetta.protocols.match) BfactorMultifunc (class in pyrosetta.rosetta.protocols.electron_density) Bi() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) BiasedFragmentMover (class in pyrosetta.rosetta.protocols.nonlocal) bIdealLoopClosing() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) bigbin() (pyrosetta.rosetta.protocols.frags.VallData method) BigBinConstraint (class in pyrosetta.rosetta.core.scoring.constraints) BigBinConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) bin() (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) bin6() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) bin_center_point() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) bin_from_index() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) bin_index() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) bin_index_hasher (class in pyrosetta.rosetta.numeric.geometry.hashing) bin_name() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) bin_params_file_name() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method)

bin_widths() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) BinarySilentStructCreator (class in pyrosetta.rosetta.core.io.silent) bind_method() (in module pyrosetta.bindings.utility) (in module pyrosetta.util) bind_property() (in module pyrosetta.bindings.utility) BindingSiteConstraintCreator (class in pyrosetta.rosetta.protocols.constraints_additional) binname() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) binner() (pyrosetta.rosetta.protocols.match.HitHasher method) BinSelector (class in pyrosetta.rosetta.core.select.residue_selector) bit_is_set() (in module pyrosetta.rosetta.core.pack.dunbrack) bit_or() (in module pyrosetta.rosetta.ObjexxFCL.bit) bite() (in module pyrosetta.rosetta.ObjexxFCL.format) blank() (in module pyrosetta.rosetta.ObjexxFCL) blanket_assign_state_0() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) BlankMatrixMult() (in module pyrosetta.rosetta.numeric.model_quality) block() (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.utility.signals.Link method) block_allocation_error_message() (in module pyrosetta.rosetta.utility.graph) block_signals() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) blocked() (pyrosetta.rosetta.utility.signals.Link method) blocking_signals() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) BlueprintArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) BOGUS_ATOM_ID() (pyrosetta.rosetta.core.id.AtomID method) BOGUS_DOF_ID() (pyrosetta.rosetta.core.id.DOF_ID method) BOGUS_NAMED_ATOM_ID() (pyrosetta.rosetta.core.id.NamedAtomID method) BOGUS_STUB_ID() (pyrosetta.rosetta.core.id.StubID method) BOGUS_TORSION_ID() (pyrosetta.rosetta.core.id.TorsionID method) boltz_rank() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) boltzmann() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) boltzmann_accept_probability() (in module pyrosetta.rosetta.numeric) boltzmann_result() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) Bond (class in pyrosetta.rosetta.core.chemical) bond() (pyrosetta.rosetta.core.chemical.ResidueType method) bond_angle() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) bond_angle_central_atoms_to_score() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) bond_angle_dof_id() (pyrosetta.rosetta.core.kinematics.AtomTree method) bond_angle_residue_type_param_set() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) bond_length() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) bond_length_dof_id() (pyrosetta.rosetta.core.kinematics.AtomTree method) bond_name() (pyrosetta.rosetta.core.chemical.Bond method) bondangle() (in module pyrosetta.rosetta.numeric.kinematic_closure) (in module pyrosetta.rosetta.numeric.kinematic_closure.radians) (pyrosetta.rosetta.core.chemical.ResidueType method) BondAnglePerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) bondangles_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) BondAromaticity (class in pyrosetta.rosetta.core.chemical) BondConjugability (class in pyrosetta.rosetta.core.chemical) bonded_neighbor() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) bonded_neighbor_all_res() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) bonded_orbitals() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) BondedAtom (class in pyrosetta.rosetta.core.kinematics.tree) BondedResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) BondID (class in pyrosetta.rosetta.core.id) bonding_distance_threshold() (in module pyrosetta.rosetta.core.io.pose_from_sfr) BondIsometry (class in pyrosetta.rosetta.core.chemical) BondName (class in pyrosetta.rosetta.core.chemical) BondOrder (class in pyrosetta.rosetta.core.chemical) BondRingness (class in pyrosetta.rosetta.core.chemical) boolean_operations (class in pyrosetta.rosetta.protocols.filters) (class in pyrosetta.rosetta.protocols.task_operations) BooleanOption (class in pyrosetta.rosetta.utility.options) BooleanOptionKey (class in pyrosetta.rosetta.utility.options) BooleanVectorOption (class in pyrosetta.rosetta.utility.options) BooleanVectorOptionKey (class in pyrosetta.rosetta.utility.options) bools_from_sizes() (in module pyrosetta.rosetta.protocols.motifs) boost_closure_cycles() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) bootstrapCATrace() (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) BorderFlag (class in pyrosetta.rosetta.numeric.interpolation.spline) born_radius() (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) bound_struct() (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) boundary_left() (pyrosetta.rosetta.core.kinematics.FoldTree method) boundary_right() (pyrosetta.rosetta.core.kinematics.FoldTree method) bounded() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) bounded_loops_from_alignment() (in module pyrosetta.rosetta.protocols.comparative_modeling) bounded_protocol() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) bounded_value() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) bounding_box() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) bounding_volume_from_index() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) bpdefs2map() (in module pyrosetta.rosetta.protocols.motifs) bQuickTest() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) BR() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) branch_connect_atom_names() (pyrosetta.rosetta.core.chemical.ResidueType method) branch_connect_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) branch_variant_type_from_atom_name() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) branch_variant_type_from_position() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) BranchCoef1 (class in pyrosetta.rosetta.protocols.branch_angle) BranchCoef2 (class in pyrosetta.rosetta.protocols.branch_angle) BranchEnergy (class in pyrosetta.rosetta.core.scoring.methods) branching_atomid1() (in module pyrosetta.rosetta.protocols.branch_angle) branching_atomids2() (in module pyrosetta.rosetta.protocols.branch_angle) branchopt() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) BranchParam1 (class in pyrosetta.rosetta.protocols.branch_angle) BranchParam2 (class in pyrosetta.rosetta.protocols.branch_angle) break_disulfide() (in module pyrosetta.rosetta.core.conformation) break_side() (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) break_side_ramp() (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) BRENT() (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) BrentLineMinimization (class in pyrosetta.rosetta.core.optimization) Bridge (class in pyrosetta.rosetta.protocols.forge.build) bridge_objects() (in module pyrosetta.rosetta.numeric.kinematic_closure.radians) bridge_res() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) BridgeChainsMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) bridgeObjects() (in module pyrosetta.rosetta.numeric.kinematic_closure) bridgeObjects_nonredundant() (in module pyrosetta.rosetta.numeric.kinematic_closure) broker() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) broker_file() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) Broker_main() (in module pyrosetta.rosetta.protocols.abinitio) brute_move_large() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) brute_move_small() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) brute_move_small_top25() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) BSAF_mode (class in pyrosetta.rosetta.protocols.simple_filters) BT_PROPERTIES (class in pyrosetta.rosetta.core.scoring.bin_transitions) BTSB_SUBBIN_TYPE (class in pyrosetta.rosetta.core.scoring.bin_transitions) buf() (pyrosetta.logging_support.PythonLoggingSink method) (pyrosetta.rosetta.basic.PyTracer method) buffer_signals() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) buffer_size() (pyrosetta.rosetta.utility.io.ozstream method) buffering_signals() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) build() (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) build_anchorless_water_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_and_discard_first_round_hits_at_all_positions() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) build_atom_ideal() (pyrosetta.rosetta.core.conformation.Residue method) build_backbone_point_water_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_base_rotamers() (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) build_centroid_loop() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) build_chemical_edge() (in module pyrosetta.rosetta.core.conformation) build_dependent_rotamers() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) build_dependent_water_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_dna_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_fake_xyz() (pyrosetta.rosetta.core.kinematics.Stub method) build_fold_tree() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) build_from_three_coords() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) build_full_model() (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo) build_fullatom_loop() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) build_helix() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) build_hits_at_all_positions() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) build_independent_water_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_init_pose() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) build_jump_edge() (in module pyrosetta.rosetta.core.conformation) build_orbital_xyz() (pyrosetta.rosetta.core.conformation.Residue method) build_point() (pyrosetta.rosetta.protocols.match.Matcher method) build_polymer_edge() (in module pyrosetta.rosetta.core.conformation) build_pose() (in module pyrosetta.rosetta.core.import_pose) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder method) build_pose_as_is() (in module pyrosetta.rosetta.core.import_pose) build_pose_as_is2() (in module pyrosetta.rosetta.core.import_pose) build_pose_from_pdb_as_is() (in module pyrosetta.rosetta.core.io.pdb) build_pwat_rotamers() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) build_random_dna_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_receptor_peptide_pose() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) build_residue_tree() (in module pyrosetta.rosetta.core.conformation) build_rna_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_rot_matrix() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) build_rot_matrix_for_pose() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) build_rotamer_list() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) build_rotamers() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) build_rotamers_from_rotamer_bins() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_rotamers_lite() (in module pyrosetta.rosetta.protocols.motifs) build_rotated_water_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) build_structures() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) build_tree() (in module pyrosetta.rosetta.core.conformation) buildable() (pyrosetta.rosetta.core.chemical.ICoorAtomID method) BuildAlaPose (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) BuildDeNovoBackboneMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) BuildInstruction (class in pyrosetta.rosetta.protocols.forge.build) BuildManager (class in pyrosetta.rosetta.protocols.forge.build) BuildSet (class in pyrosetta.rosetta.protocols.match.upstream) buildsturm() (in module pyrosetta.rosetta.numeric.kinematic_closure) built_atom_vertex() (pyrosetta.rosetta.core.chemical.AtomICoor method) bulge_keyname() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) bump_check() (in module pyrosetta.rosetta.core.pack.rotamer_set) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) bump_check_backbone() (pyrosetta.rosetta.core.scoring.ScoreFunction method) bump_check_full() (pyrosetta.rosetta.core.scoring.ScoreFunction method) bump_energy_backbone() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) bump_energy_full() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) bump_filter() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) bump_grid() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) bump_grid_to_enclose_pose() (in module pyrosetta.rosetta.protocols.match) bump_grid_to_enclose_residue() (in module pyrosetta.rosetta.protocols.match) bump_grid_to_enclose_residue_backbone() (in module pyrosetta.rosetta.protocols.match) BumpSelectorDecision (class in pyrosetta.rosetta.core.pack.rotamer_set) bundle_symmetry() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) bundle_symmetry_copies() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) BundleGridSamplerHelper (class in pyrosetta.rosetta.protocols.helical_bundle) BundleParameters (class in pyrosetta.rosetta.protocols.helical_bundle.parameters) BundleParametersSet (class in pyrosetta.rosetta.protocols.helical_bundle.parameters) BundleReporterFilterBehaviour (class in pyrosetta.rosetta.protocols.helical_bundle) burial_sigmoid() (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) burial_threshold() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions method) buried_unsatisfied_penalty_burial_threshold() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) buried_unsatisfied_penalty_cone_angle_exponent() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) buried_unsatisfied_penalty_cone_angle_shift_factor() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) buried_unsatisfied_penalty_cone_dist_exponent() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) buried_unsatisfied_penalty_cone_dist_midpoint() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) buried_unsatisfied_penalty_hbond_energy_threshold() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) BuriedSurfaceAreaFilter (class in pyrosetta.rosetta.protocols.simple_filters) BuriedUnsatHbondFilter (class in pyrosetta.rosetta.protocols.simple_filters) BuriedUnsatPenalty (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty) BuriedUnsatPenaltyEdge (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph) BuriedUnsatPenaltyGraph (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph) BuriedUnsatPenaltyGraphContainer (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph) BuriedUnsatPenaltyGraphHbond (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph) BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph) BuriedUnsatPenaltyGraphOptions (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph) BuriedUnsatPenaltyNode (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph) BuriedUnsatPenaltyNodeData (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph) byte (class in pyrosetta.rosetta.ObjexxFCL)

C

C() (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) c0() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) c1() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) c1prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) c2() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) c2prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) c3() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) c3prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) c4prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) c5prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) c_alpha_index() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) c_array_mult() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) C_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) c_beta_index() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) c_mult_ip() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) c_n() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) c_n_bond() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) c_n_ca() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) c_n_ca_angle() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) c_segment() (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) c_str() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) c_terminal_constraint_strength() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) c_terminus_size() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) c_xyz() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) CA() (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) CA_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) ca_c() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) ca_c_bond() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) ca_c_n() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) ca_c_n_angle() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) Ca_coords() (in module pyrosetta.rosetta.protocols.protein_interface_design.filters) CA_gdtmm() (in module pyrosetta.rosetta.core.scoring) CA_gdttm() (in module pyrosetta.rosetta.core.scoring) CA_maxsub() (in module pyrosetta.rosetta.core.scoring) CA_or_equiv_rmsd() (in module pyrosetta.rosetta.core.scoring) CA_rmsd() (in module pyrosetta.rosetta.core.scoring) CA_rmsd_symmetric() (in module pyrosetta.rosetta.core.scoring) CA_Sscore() (in module pyrosetta.rosetta.protocols.mpi_refinement) CA_superimpose() (in module pyrosetta.rosetta.protocols.toolbox) ca_xyz() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) CaCbCb_Angle_Func (class in pyrosetta.rosetta.core.scoring.disulfides) CaCbCbCa_Dihedral_Func (class in pyrosetta.rosetta.core.scoring.disulfides) cache() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) cache_fragments() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) cache_limit() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) cache_pose() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) cache_profile() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) cache_resfile() (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) cache_tag() (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) cache_task() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) CacheableAtomID_MapVector (class in pyrosetta.rosetta.core.id) CacheableData (class in pyrosetta.rosetta.basic.datacache) CacheableObserver (class in pyrosetta.rosetta.core.pose.datacache) CacheableObserverType (class in pyrosetta.rosetta.core.pose.datacache) CacheablePoseRawPtr (class in pyrosetta.rosetta.core.pose.datacache) CacheableResidueTypeSets (class in pyrosetta.rosetta.core.chemical) CacheableString (class in pyrosetta.rosetta.basic.datacache) CacheableStringFloatMap (class in pyrosetta.rosetta.basic.datacache) CacheableStringIntegerMap (class in pyrosetta.rosetta.basic.datacache) CacheableStringMap (class in pyrosetta.rosetta.basic.datacache) cached_score() (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) cal_delta_internal_coordinates() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) cal_delta_internal_coordinates_squared() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) cal_dis_angle_to_find_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) cal_distance() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) cal_distance_squared() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) cal_min_avg_dis_between_sheets_by_cen_res() (in module pyrosetta.rosetta.protocols.features.strand_assembly) cal_min_avg_dis_between_two_sheets_by_cen_res() (in module pyrosetta.rosetta.protocols.features.strand_assembly) cal_min_dis_between_sheets_by_all_res() (in module pyrosetta.rosetta.protocols.features.strand_assembly) cal_min_dis_between_two_sheets_by_all_res() (in module pyrosetta.rosetta.protocols.features.strand_assembly) cal_num_of_sheets_that_surround_this_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) cal_shortest_dis_between_facing_aro_in_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) Calc() (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) calc_all_averages() (in module pyrosetta.rosetta.protocols.unfolded_state_energy_calculator) calc_all_dist() (in module pyrosetta.rosetta.protocols.make_rot_lib) calc_angle_rmsd() (in module pyrosetta.rosetta.protocols.membrane) calc_bb_boltz_probs() (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) calc_boltz_score() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) calc_CA_Irmsd() (in module pyrosetta.rosetta.protocols.docking) calc_centroids() (in module pyrosetta.rosetta.protocols.make_rot_lib) calc_delta_sasa() (in module pyrosetta.rosetta.protocols.fldsgn.topology) calc_dihedral() (in module pyrosetta.rosetta.protocols.denovo_design.movers) (in module pyrosetta.toolbox.numpy_utils) calc_dist() (in module pyrosetta.rosetta.protocols.make_rot_lib) calc_energy() (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) calc_exp_value_rot_matrix() (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) calc_Fnat() (in module pyrosetta.rosetta.protocols.docking) calc_Fnonnat() (in module pyrosetta.rosetta.protocols.docking) calc_geometry() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) calc_helix_axis() (in module pyrosetta.rosetta.protocols.membrane) calc_helix_tilt_angle() (in module pyrosetta.rosetta.protocols.membrane) calc_interacting_vector() (in module pyrosetta.rosetta.core.select.util) calc_interaction_energy() (in module pyrosetta.rosetta.protocols.docking) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) calc_interface_vector() (in module pyrosetta.rosetta.core.select.util) calc_intf_score() (in module pyrosetta.rosetta.protocols.docking) calc_Irmsd() (in module pyrosetta.rosetta.protocols.docking) calc_kl_divergence() (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) calc_Lrmsd() (in module pyrosetta.rosetta.protocols.docking) calc_P1rmsd() (in module pyrosetta.rosetta.protocols.docking) calc_P2rmsd() (in module pyrosetta.rosetta.protocols.docking) calc_per_atom_sasa() (in module pyrosetta.rosetta.core.scoring) calc_per_atom_sasa_sc() (in module pyrosetta.rosetta.core.scoring) calc_per_res_hydrophobic_sasa() (in module pyrosetta.rosetta.core.scoring) calc_product() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser method) calc_quadratic() (in module pyrosetta.rosetta.basic) calc_res_contact() (in module pyrosetta.rosetta.protocols.docking) calc_residue_burial() (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) calc_rms() (in module pyrosetta.rosetta.numeric.model_quality) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) calc_rms_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) calc_rnp_pair_dist_score() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPairDistPotential method) calc_rotamer_clusters() (in module pyrosetta.rosetta.protocols.make_rot_lib) calc_rsd_sasa() (in module pyrosetta.rosetta.protocols.forge.methods) calc_score() (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) calc_std_dev() (in module pyrosetta.rosetta.protocols.make_rot_lib) calc_strand_helix_angle() (in module pyrosetta.rosetta.protocols.fldsgn.topology) calc_strand_pairing_set() (in module pyrosetta.rosetta.protocols.fldsgn.topology) calc_total_sasa() (in module pyrosetta.rosetta.core.scoring) calc_vector_boltzmann() (in module pyrosetta.rosetta.protocols.unfolded_state_energy_calculator) calc_vector_mean() (in module pyrosetta.rosetta.protocols.unfolded_state_energy_calculator) calc_vector_median() (in module pyrosetta.rosetta.protocols.unfolded_state_energy_calculator) calc_vector_mode() (in module pyrosetta.rosetta.protocols.unfolded_state_energy_calculator) CalcInterNeighborGroup (class in pyrosetta.rosetta.protocols.toolbox) CalcSc() (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) calculate() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.TotalEnergyMetric method) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) calculate_atom_id_domain_map() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) calculate_axes() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) calculate_center_xyz() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) calculate_chi2_free() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) calculate_dihedral_distance() (in module pyrosetta.rosetta.numeric.model_quality) (in module pyrosetta.rosetta.protocols.antibody.clusters) calculate_dihedral_w_4_resnums() (in module pyrosetta.rosetta.protocols.features.strand_assembly) calculate_energy() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) calculate_frh_frl() (in module pyrosetta.rosetta.protocols.antibody.grafting) calculate_geometry() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) calculate_highres_ref_energy() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) calculate_I_of_E() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) calculate_interface_score() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) calculate_intra_res_hbonds() (in module pyrosetta.rosetta.core.scoring.hbonds) calculate_inverting_virtuals() (in module pyrosetta.rosetta.core.conformation.symmetry) calculate_jacobians() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) calculate_lowres_ref_energy() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) calculate_neighbor_table() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) calculate_penalty_once_almost_from_scratch_using_reference_graph() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) calculate_penalty_once_from_scratch() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) calculate_per_residue_interface_score() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) calculate_plane_axes() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) calculate_point_in_cone() (in module pyrosetta.rosetta.core.select.util) calculate_rigid_matrix() (in module pyrosetta.rosetta.core.chemical) calculate_score() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) calculate_stability_metric() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) calculate_statistics() (in module pyrosetta.rosetta.protocols.ncbb) calculate_total_cst_score() (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) calculate_water_overcoordinated_hb_correction() (in module pyrosetta.rosetta.protocols.hydrate) calculated() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) calculator_id() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) CALIBRATION_ATOM_TYPE (class in pyrosetta.rosetta.protocols.noesy_assign) calibration_atom_type() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) call_output_observers() (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) call_setup() (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) calpha_superimpose_pose() (in module pyrosetta.rosetta.core.scoring) calpha_superimpose_with_mapping() (in module pyrosetta.rosetta.core.sequence) CamShiftEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) can_be_deleted() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) can_hold_another() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) cancel_batches_previous_to() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) candidate_res_atoms_reqd_near_target_atom() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) CandidatesCollector (class in pyrosetta.rosetta.protocols.frag_picker) canonical() (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepLibrary method) canonical_atom_aliases() (pyrosetta.rosetta.core.chemical.ResidueType method) canonical_atom_count() (in module pyrosetta.rosetta.core.pose) canonical_base_pair_step_library() (pyrosetta.rosetta.core.import_pose.libraries.RNA_LibraryManager method) canonical_residue_count() (in module pyrosetta.rosetta.core.pose) canonical_sampling_main() (in module pyrosetta.rosetta.protocols.canonical_sampling) canonicalize() (in module pyrosetta.rosetta.protocols.denovo_design.components) capacity() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) carbohydrate_info() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) CarbohydrateInfoManager (class in pyrosetta.rosetta.core.chemical.carbohydrates) carry_out_filtering() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) cart_min() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) cart_numerical_derivative_check() (in module pyrosetta.rosetta.core.optimization) cartesian() (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) cartesian_collect_atompairE_deriv() (in module pyrosetta.rosetta.core.optimization) cartesian_collect_torsional_deriv() (in module pyrosetta.rosetta.core.optimization) cartesian_dfunc() (in module pyrosetta.rosetta.core.optimization) CartesianBondedEnergy (class in pyrosetta.rosetta.core.scoring.methods) CartesianMinimizer (class in pyrosetta.rosetta.core.optimization) CartesianMultifunc (class in pyrosetta.rosetta.core.optimization) case_from_lines() (in module pyrosetta.rosetta.core.chemical) catalog() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) catalytic_res() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) CatmullRomSplineBoundaryType (class in pyrosetta.rosetta.numeric.interpolation) CB() (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) CB_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) cb_dist_cut() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) CB_dist_cutoff() (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) Cb_Distance_Func (class in pyrosetta.rosetta.core.scoring.disulfides) cb_force() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) cb_weight() (in module pyrosetta.rosetta.protocols.sic_dock) cb_weight_map_from_pose() (in module pyrosetta.rosetta.protocols.sic_dock) cb_weights_from_map() (in module pyrosetta.rosetta.protocols.sic_dock) cb_weights_from_pose() (in module pyrosetta.rosetta.protocols.sic_dock) cbx() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) cby() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) cbz() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) ccd_angle() (in module pyrosetta.rosetta.numeric) ccd_close() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) ccd_close_loops() (in module pyrosetta.rosetta.protocols.loops) CCDEndsGraftMover (class in pyrosetta.rosetta.protocols.grafting) CCDLoopClosureMover (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) CCDLoopClosureMoverCreator (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) CCluster (class in pyrosetta.rosetta.protocols.pockets) CClusterSet (class in pyrosetta.rosetta.protocols.pockets) CD (class in pyrosetta) cd_1b_types() (pyrosetta.rosetta.core.scoring.ScoreFunction method) cd_2b_begin() (pyrosetta.rosetta.core.scoring.ScoreFunction method) cd_2b_end() (pyrosetta.rosetta.core.scoring.ScoreFunction method) cd_2b_intrares_begin() (pyrosetta.rosetta.core.scoring.ScoreFunction method) cd_2b_intrares_end() (pyrosetta.rosetta.core.scoring.ScoreFunction method) cd_2b_types() (pyrosetta.rosetta.core.scoring.ScoreFunction method) cd_lr_2b_methods_begin() (pyrosetta.rosetta.core.scoring.ScoreFunction method) cd_lr_2b_methods_end() (pyrosetta.rosetta.core.scoring.ScoreFunction method) cd_lr_2b_types() (pyrosetta.rosetta.core.scoring.ScoreFunction method) cdr() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) cdr1_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) cdr2_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) cdr3_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) cdr_cluster_enum_to_string() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) cdr_cluster_is_present() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) cdr_cluster_string_to_enum() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) cdr_CN_anchor_distance() (in module pyrosetta.rosetta.protocols.antibody) cdr_definition_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_definition_is_present() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_definition_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) CDR_Detector (class in pyrosetta.rosetta.protocols.antibody.grafting) cdr_energy() (in module pyrosetta.rosetta.protocols.antibody) CDR_H3_cter_filter() (in module pyrosetta.rosetta.protocols.antibody) CDR_H3_filter() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) CDR_H3_filter_legacy_code_with_old_rule() (in module pyrosetta.rosetta.protocols.antibody) cdr_has_res_constraints() (in module pyrosetta.rosetta.protocols.antibody.constraints) cdr_landmark_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_landmark_is_present() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_landmark_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_name_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_name_is_present() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_name_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_overhang() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) CDRCluster (class in pyrosetta.rosetta.protocols.antibody.clusters) CDRClusterEnum (class in pyrosetta.rosetta.protocols.antibody.clusters) CDRClusterEnumManager (class in pyrosetta.rosetta.protocols.antibody.clusters) CDRClusterMatcher (class in pyrosetta.rosetta.protocols.antibody.clusters) CDRClusterSet (class in pyrosetta.rosetta.protocols.antibody.clusters) CDRDefinitionEnum (class in pyrosetta.rosetta.protocols.antibody) CDRDihedralConstraintMover (class in pyrosetta.rosetta.protocols.antibody.constraints) CDRGraftDesignOptions (class in pyrosetta.rosetta.protocols.antibody.design) CDRH3Modeler (class in pyrosetta.rosetta.protocols.antibody_legacy) CDRLandmarkEnum (class in pyrosetta.rosetta.protocols.antibody) CDRNameEnum (class in pyrosetta.rosetta.protocols.antibody) CDRResidueSelector (class in pyrosetta.rosetta.protocols.antibody.residue_selector) CDRSetOptions (class in pyrosetta.rosetta.protocols.antibody) CDRSetOptionsParser (class in pyrosetta.rosetta.protocols.antibody) cen_dist10_pad() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist10_pad_hinv() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist10_pad_minus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist10_pad_plus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist12_pad() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist12_pad_hinv() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist12_pad_minus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist12_pad_plus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist5_pad() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist5_pad_hinv() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist5_pad_minus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist5_pad_plus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist6_pad() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist6_pad_hinv() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist6_pad_plus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist7_pad() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist7_pad_hinv() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist7_pad_minus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist7_pad_plus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) Cen_Distance_Func (class in pyrosetta.rosetta.core.scoring.disulfides) Cend_orient() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) Cend_pos() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) cenfilter() (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) cenlist_from_pose() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) CenListInfo (class in pyrosetta.rosetta.core.scoring) CenrotLibrary (class in pyrosetta.rosetta.core.pack.dunbrack.cenrot) center() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.core.id.NamedStubID method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.kinematics.Stub method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) center_of_geom() (in module pyrosetta.rosetta.protocols.sic_dock) center_of_mass() (in module pyrosetta.rosetta.core.pose) (in module pyrosetta.rosetta.protocols.geometry) (pyrosetta.rosetta.protocols.loops.Loops method) center_residues() (in module pyrosetta.rosetta.protocols.cluster.calibur) centered() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) central_residue() (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborsByDistanceCalculator method) central_residue_group_selector() (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) central_residues() (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborhoodByDistanceCalculator method) centroid() (in module pyrosetta.rosetta.core.pack) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) centroid_by_chain() (in module pyrosetta.rosetta.protocols.geometry) centroid_by_chains() (in module pyrosetta.rosetta.protocols.geometry) centroid_by_residues() (in module pyrosetta.rosetta.protocols.geometry) centroid_dist() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) centroid_neighbors() (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) centroid_output() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) centroid_pair_by_jump() (in module pyrosetta.rosetta.protocols.geometry) centroid_pose_from_pdb() (in module pyrosetta.rosetta.core.import_pose) centroid_scatter() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) centroid_score_diff_cut() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) centroid_scorefxn() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) centroid_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) centroid_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) centroid_weights() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) CentroidDisulfideEnergyComponents (class in pyrosetta.rosetta.core.scoring.disulfides) CentroidDisulfideNeighborConstIterator (class in pyrosetta.rosetta.core.scoring.disulfides) CentroidDisulfideNeighborIterator (class in pyrosetta.rosetta.core.scoring.disulfides) CentroidDisulfidePotential (class in pyrosetta.rosetta.core.scoring.disulfides) CentroidRelax (class in pyrosetta.rosetta.protocols.relax) CentroidRotamerSampleData (class in pyrosetta.rosetta.core.pack.dunbrack.cenrot) centroids_by_jump() (in module pyrosetta.rosetta.protocols.geometry) centroids_by_jump_int() (in module pyrosetta.rosetta.protocols.geometry) CentroidScatter (class in pyrosetta.rosetta.core.scoring.fiber_diffraction) cenx() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) ceny() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) cenz() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) cfg_nd() (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) cfg_r() (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) chain() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) chain_begin() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) chain_com() (in module pyrosetta.rosetta.protocols.membrane) chain_cut() (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) chain_end() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) chain_end_res() (in module pyrosetta.rosetta.core.pose) chain_endings() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) chain_gws_string() (in module pyrosetta.rosetta.core.io.carbohydrates) chain_id() (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) chain_lt (class in pyrosetta.rosetta.protocols.pose_length_moves) chain_num() (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) chain_pair_pose_prepared() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) chain_sequence() (pyrosetta.rosetta.core.pose.Pose method) chain_sequences() (pyrosetta.rosetta.core.io.StructFileRep method) chain_tm_com() (in module pyrosetta.rosetta.protocols.membrane) ChainBreak (class in pyrosetta.rosetta.protocols.simple_filters) CHAINBREAK_BOGUS_ATOM_ID() (pyrosetta.rosetta.core.id.AtomID method) CHAINBREAK_BOGUS_NAMED_ATOM_ID() (pyrosetta.rosetta.core.id.NamedAtomID method) ChainbreakEnergy (class in pyrosetta.rosetta.core.scoring.methods) chainbreaks() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) ChainCountFilter (class in pyrosetta.rosetta.protocols.simple_filters) ChainDirection (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) ChainedSolutionList (class in pyrosetta.rosetta.protocols.kinematic_closure) chainID() (pyrosetta.rosetta.core.io.ResidueInformation method) chains() (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) chains_from_termini() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) chains_in_full_model() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) chains_whose_residues_are_separate_chemical_entities() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) ChainSplitMover (class in pyrosetta.rosetta.protocols.simple_moves) chainXYZ() (in module pyrosetta.rosetta.numeric.kinematic_closure) (in module pyrosetta.rosetta.numeric.kinematic_closure.radians) change_bond_type() (pyrosetta.rosetta.core.chemical.ResidueType method) change_chi_without_replacing_residue() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) change_conformation() (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) change_cys_state() (in module pyrosetta.rosetta.core.conformation) change_foldtree() (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) change_sheet_id_if_possible() (in module pyrosetta.rosetta.protocols.features.strand_assembly) change_weight() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) ChangeAndResetFoldTreeMover (class in pyrosetta.rosetta.protocols.simple_moves) ChangeBondType (class in pyrosetta.rosetta.core.chemical) changed() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) changes_connections_on() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.RenameAtom method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.Set_AA method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) channel() (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerImpl method) channel_color() (pyrosetta.rosetta.basic.TracerImpl method) channel_name_color() (pyrosetta.rosetta.basic.TracerImpl method) CHAR() (in module pyrosetta.rosetta.ObjexxFCL.Fortran) char_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) char_to_int() (in module pyrosetta.rosetta.core.io.carbohydrates) char_type() (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) char_valid_as_torsion_bin() (in module pyrosetta.rosetta.core.conformation) charge() (pyrosetta.rosetta.core.chemical.Atom method) ChargeAtom (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) ChargeChargeFeaturesCreator (class in pyrosetta.rosetta.protocols.features) CHARGED (class in pyrosetta.rosetta.core.pack.task) charged() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) CharmmPeriodicFunc (class in pyrosetta.rosetta.core.scoring.func) check() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) check_all_ligand_atoms() (in module pyrosetta.rosetta.protocols.ligand_docking.ligand_options) check_all_residues_sampled() (in module pyrosetta.rosetta.core.pose.full_model_info) check_and_correct_sister_atom_based_on_chirality() (in module pyrosetta.rosetta.core.io.pose_from_sfr) check_and_correct_sister_atom_based_on_outgroup() (in module pyrosetta.rosetta.core.io.pose_from_sfr) check_and_correct_sister_atoms() (in module pyrosetta.rosetta.core.io.pose_from_sfr) check_base_pair() (in module pyrosetta.rosetta.protocols.rna.denovo) check_binary_chars() (in module pyrosetta.rosetta.core.io.serialization) check_binary_unsigned_int() (in module pyrosetta.rosetta.core.io.serialization) check_bounds() (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) check_can_append() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) check_can_prepend() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) check_canonicalness_of_LR() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_canonicalness_of_PA() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_canonicalness_of_parallel_EE() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_cb() (in module pyrosetta.rosetta.protocols.antibody.design) check_clear_for_stacking() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) check_closure() (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) check_consistency() (pyrosetta.rosetta.core.conformation.signals.LengthEvent method) check_deprecated_flags() (in module pyrosetta.rosetta.core.init) check_domain_map() (pyrosetta.rosetta.core.scoring.NeighborList method) check_edges_for_atom_info() (pyrosetta.rosetta.core.kinematics.FoldTree method) check_extra_minimize_res_are_input() (in module pyrosetta.rosetta.core.import_pose) check_fa_dun() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) check_filters() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) check_fix_aho_cdr_numbering() (in module pyrosetta.rosetta.protocols.antibody) check_fold_tree() (pyrosetta.rosetta.core.kinematics.FoldTree method) check_fold_tree_OK() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) check_for_base_neighbor() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) check_for_input_domain() (in module pyrosetta.rosetta.protocols.stepwise.modeler) check_for_messed_up_structure() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) check_for_symmetric_peaks() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) check_forming_base_pair() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) check_forward_backward() (pyrosetta.rosetta.core.import_pose.libraries.RNA_JumpLibrary method) check_frequency() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) check_full_model_info_OK() (in module pyrosetta.rosetta.core.pose.full_model_info) check_good_cutpoint_neighbour() (in module pyrosetta.rosetta.core.conformation) check_hairpin() (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) check_heading_direction() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_helix_existence() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_if_connected_residues_belong_to_regions() (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) check_if_pose_renumbered_for_clusters() (in module pyrosetta.rosetta.protocols.antibody.clusters) check_if_proton_chi_atom() (in module pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens) check_if_residues_are_Ctermini() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) check_if_residues_are_Ntermini() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) check_in_base_pair_list() (in module pyrosetta.rosetta.core.pose.rna) check_instantiated_O2Prime_hydrogen() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) check_is_working_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) check_jump_to_next_residue_in_chain() (in module pyrosetta.rosetta.protocols.stepwise.modeler) check_jump_to_previous_residue_in_chain() (in module pyrosetta.rosetta.protocols.stepwise.modeler) check_key() (pyrosetta.rosetta.utility.options.OptionCollection method) check_kink_helix() (in module pyrosetta.rosetta.protocols.fldsgn.topology) check_load_fconfig() (in module pyrosetta.rosetta.core.init) check_loops() (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) check_LR() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_membrane_fold_tree() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) check_methods_in_right_order() (pyrosetta.rosetta.core.scoring.ScoreFunction method) check_mmt() (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) check_neighbor_ligand_atom() (in module pyrosetta.rosetta.protocols.ligand_docking.ligand_options) check_orientation() (in module pyrosetta.rosetta.protocols.membrane) check_overlap() (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) check_PA() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_phosphate_contacts_donor() (in module pyrosetta.rosetta.core.pose.rna) check_pleat() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) check_pose_tree_compatibility() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) check_rama() (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) check_rama2() (pyrosetta.rosetta.core.sequence.ABEGO method) check_rama_scores() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) check_range() (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) check_relevant_residues() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) check_relevant_residues_range() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) check_restricted_access() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) check_rna_loop() (in module pyrosetta.rosetta.core.scoring.rna) check_sample_sugar_in_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) check_score() (in module pyrosetta.rosetta.protocols.ligand_docking) check_score_function_sanity() (in module pyrosetta.rosetta.core.scoring) check_scorefxn_has_constraint_terms_if_pose_has_constraints() (in module pyrosetta.rosetta.protocols.stepwise.modeler) check_setup() (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) check_specs() (pyrosetta.rosetta.utility.options.OptionCollection method) check_ss() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) check_stack() (in module pyrosetta.rosetta.core.scoring.rna) check_statement_sanity() (in module pyrosetta.rosetta.basic.database) check_status() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) check_strand_too_closeness() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_surface_area_leerichards_deriv() (in module pyrosetta.rosetta.core.scoring.packstat) check_sw_by_dis() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_valid_membrane() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) check_validity_and_get_working_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) check_value() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) check_values() (pyrosetta.rosetta.utility.options.OptionCollection method) check_vector() (in module pyrosetta.rosetta.protocols.membrane) check_watson_crick_sequence() (in module pyrosetta.rosetta.core.scoring.rna) check_whether_hairpin_connects_short_strand() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_same_direction_strands_connect_two_sheets_or_a_loop() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_sheets_are_connected_with_near_bb_atoms() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_strand_i_is_in_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_sw_by_sh_id_still_alive() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_sw_is_not_connected_with_continuous_atoms() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_this_pdb_should_be_excluded() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_this_sheet_is_too_short() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_working_res() (in module pyrosetta.rosetta.core.import_pose) checkpoint() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) checkpoint_cleanup() (in module pyrosetta.rosetta.protocols.dna) checkpoint_exists() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) checkpoint_file() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) checkpoint_with_interval() (in module pyrosetta.rosetta.protocols.checkpoint) ChemicalManager (class in pyrosetta.rosetta.core.chemical) ChemicalShiftAnisotropy (class in pyrosetta.rosetta.core.scoring) ChemicalShiftData (class in pyrosetta.rosetta.core.scoring.rna.chemical_shift) ChemicalShiftEvaluatorCreator (class in pyrosetta.rosetta.protocols.sparta) chemshift_compliance() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) CheshireCell (class in pyrosetta.rosetta.protocols.cryst) chi() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) chi1_torsion_atom() (in module pyrosetta.rosetta.core.chemical.rna) chi1_torsion_atom_index() (in module pyrosetta.rosetta.core.chemical.rna) chi2max() (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation method) chi2min() (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation method) chi_2_proton_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) chi_atom_vds() (pyrosetta.rosetta.core.chemical.ResidueType method) chi_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) chi_north_anti() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) chi_north_syn() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) chi_number_pseudoalpha() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) chi_number_pseudobeta() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) chi_number_pseudoepsilon() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) chi_number_pseudogamma() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) chi_number_pseudozeta() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) chi_rotamers() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) chi_south_anti() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) chi_south_syn() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) CHIDihedralSamplingData (class in pyrosetta.rosetta.core.scoring.carbohydrates) CHIEnergyFunction (class in pyrosetta.rosetta.core.scoring.carbohydrates) CHIEnergyFunctionLinkageType (class in pyrosetta.rosetta.core.scoring.carbohydrates) child() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) child_index() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) chinum() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) ChiralFlipAtoms (class in pyrosetta.rosetta.core.chemical) ChiralFlipNaming (class in pyrosetta.rosetta.core.chemical) Chirality (class in pyrosetta.rosetta.protocols.simple_moves.chiral) ChiState (class in pyrosetta.rosetta.core.chemical.rna) ChiStrategy (class in pyrosetta.rosetta.protocols.match.upstream) chitip_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) chitip_atoms() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) ChiWellRmsdEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) choices() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) choose() (pyrosetta.rosetta.protocols.nonlocal.Chunk method) (pyrosetta.rosetta.protocols.nonlocal.Policy method) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy method) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy method) choose_best_solution_based_on_score_function() (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) choose_canonical() (in module pyrosetta.rosetta.protocols.denovo_design.components) choose_cutpoint() (pyrosetta.rosetta.protocols.loops.Loop method) choose_cutpoints() (pyrosetta.rosetta.protocols.loops.Loops method) choose_effective_sequence_separation() (in module pyrosetta.rosetta.core.scoring.constraints) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) choose_fragment() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) choose_hbond_parameter_set() (in module pyrosetta.rosetta.protocols.simple_pose_metric_calculators) choose_least_perturb_solution() (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) choose_n_best() (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) choose_random() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) choose_random_if_unspecified_nucleotide() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) choose_randomly_from_allowed_at_position() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) choose_window_length() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) choose_window_start() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) chop_fragments() (in module pyrosetta.rosetta.core.fragment) Chothia_Numberer (class in pyrosetta.rosetta.protocols.antibody.grafting) chr_chains_nonrepeated() (in module pyrosetta.rosetta.utility.tag) Chunk (class in pyrosetta.rosetta.protocols.nonlocal) chunk_coverage() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) chunk_key() (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) chunk_probabilities() (in module pyrosetta.rosetta.protocols.medal) chunk_set() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) chunk_sets() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) ChunkExponent (class in pyrosetta.rosetta.ObjexxFCL) chunks_by_CA_CA_distance() (in module pyrosetta.rosetta.protocols.nonlocal) Ci() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) ci_1b_types() (pyrosetta.rosetta.core.scoring.ScoreFunction method) ci_2b_begin() (pyrosetta.rosetta.core.scoring.ScoreFunction method) ci_2b_end() (pyrosetta.rosetta.core.scoring.ScoreFunction method) ci_2b_intrares_begin() (pyrosetta.rosetta.core.scoring.ScoreFunction method) ci_2b_intrares_end() (pyrosetta.rosetta.core.scoring.ScoreFunction method) ci_2b_types() (pyrosetta.rosetta.core.scoring.ScoreFunction method) ci_lr_2b_methods_begin() (pyrosetta.rosetta.core.scoring.ScoreFunction method) ci_lr_2b_methods_end() (pyrosetta.rosetta.core.scoring.ScoreFunction method) ci_lr_2b_types() (pyrosetta.rosetta.core.scoring.ScoreFunction method) circle() (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) CircularGeneral1D_Func (class in pyrosetta.rosetta.core.scoring.func) CircularHarmonicFunc (class in pyrosetta.rosetta.core.scoring.func) CircularPermuteFreePeptideMover (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers) CircularPowerFunc (class in pyrosetta.rosetta.core.scoring.func) CircularSigmoidalFunc (class in pyrosetta.rosetta.core.scoring.func) cis_omega() (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) cis_omega_torsion_bin() (in module pyrosetta.rosetta.core.conformation) cis_peptide_bonds() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) cis_trans_match() (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) cispep_map() (pyrosetta.rosetta.core.io.StructFileRep method) CisPeptideInformation (class in pyrosetta.rosetta.core.io) cl_value() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) claim_accepted() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) claimer_builds_own_fold_tree() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) clashes() (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) class_key() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter method) class_name() (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) ClassicAbinitio (class in pyrosetta.rosetta.protocols.abinitio) ClassicAbinitio.StageID (class in pyrosetta.rosetta.protocols.abinitio) ClassicFragmentMover (class in pyrosetta.rosetta.protocols.simple_moves) ClassicMatchAlgorithm (class in pyrosetta.rosetta.protocols.match.downstream) ClassicRelax (class in pyrosetta.rosetta.protocols.relax) classification() (pyrosetta.rosetta.core.io.HeaderInformation method) classify_base_pairs() (in module pyrosetta.rosetta.core.pose.rna) classify_base_pairs_lores() (in module pyrosetta.rosetta.protocols.rna.denovo) classname() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.core.fragment.FragmentSetLoader method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader method) clean_for_storage() (in module pyrosetta.rosetta.protocols.denovo_design.components) clean_from_storage() (in module pyrosetta.rosetta.protocols.denovo_design.components) clean_jumps() (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) clean_residue_task() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) clean_up() (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) clean_up_after_packing() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) clean_up_residuearrayannealableenergy_after_packing() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) cleanATOM() (in module pyrosetta.toolbox) (in module pyrosetta.toolbox.cleaning) cleanCRYS() (in module pyrosetta.toolbox) (in module pyrosetta.toolbox.cleaning) cleaned() (pyrosetta.rosetta.utility.options.OptionCollection method) cleaned_alignment_file() (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) cleanup() (in module pyrosetta.rosetta.core.import_pose) clear() (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.NeighborList method) (pyrosetta.rosetta.core.scoring.Strands method) (pyrosetta.rosetta.core.scoring.TMscoreStore method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.io.FileContentsMap method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.recent_history_queue method) clear_() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) clear_all() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) clear_blacklist() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) clear_checkpoints() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) clear_chi_rotamers() (pyrosetta.rosetta.core.chemical.ResidueType method) clear_comments() (pyrosetta.rosetta.core.io.silent.SilentStruct method) clear_compounds() (pyrosetta.rosetta.core.io.HeaderInformation method) clear_conformation_viewers() (in module pyrosetta.rosetta.protocols.viewer) clear_connected_resonances() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) clear_connections() (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) clear_data() (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) clear_dependencies() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) clear_design_taskset() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) clear_edges() (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) clear_energies() (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) clear_evaluators() (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) clear_events() (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) clear_experimental_techniques() (pyrosetta.rosetta.core.io.HeaderInformation method) clear_extent_eval() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) clear_extent_gen() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) clear_external_geom_samplers() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) clear_filters() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) clear_fragment_eval() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) clear_fragment_gen() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) clear_fragments() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) clear_free_peptide_movers() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) clear_from_pose() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) clear_glycan_trees() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) clear_hash_map() (pyrosetta.rosetta.protocols.match.HitHasher method) clear_hbond_counts() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) clear_imporated_data() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser method) clear_info() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) clear_input_sources() (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) clear_inverse_rotamers() (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) clear_jumps() (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) clear_keywords() (pyrosetta.rosetta.core.io.HeaderInformation method) clear_movers() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) clear_movers_and_refiners() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) clear_mutation_sets() (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) clear_no_notify() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) clear_observers() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) clear_orbitals() (pyrosetta.rosetta.core.chemical.ResidueType method) clear_other_pose_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) clear_output() (pyrosetta.rosetta.protocols.jd2.Job method) clear_overall_prob_set() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) clear_parameters_list() (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) clear_parameters_set_list() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) clear_perturbers() (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) clear_poses() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) clear_positions() (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) clear_postfold_movers() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) clear_prefold_movers() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) clear_prob_set() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) clear_properties() (pyrosetta.rosetta.core.chemical.AtomType method) clear_rcgs() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) clear_refiners() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) clear_res_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) clear_reset_filters() (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) clear_residue_connections() (pyrosetta.rosetta.core.conformation.Residue method) clear_residues() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) clear_reslabel() (pyrosetta.rosetta.core.pose.PDBInfo method) clear_rms() (pyrosetta.rosetta.numeric.model_quality.RmsData method) clear_rna_scoring_info() (in module pyrosetta.rosetta.core.scoring.rna) clear_rna_secstruct_legacy_info() (in module pyrosetta.rosetta.core.pose.rna.secstruct_legacy) clear_rnl_pose() (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) clear_rv_infos() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) clear_segments() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) clear_sequence_constraints() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) clear_serial_data() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) clear_setup_movers() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) clear_shared_silent_data() (pyrosetta.rosetta.core.io.silent.SilentFileData method) clear_structure_map() (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) clear_task() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) clear_task_factory() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) clear_title() (pyrosetta.rosetta.core.io.HeaderInformation method) clear_torsion_string_stack() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) clear_user_provided_movers() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) clear_Vall() (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager method) ClearChiRotamers (class in pyrosetta.rosetta.core.chemical) clearPoseExtraScore() (in module pyrosetta.rosetta.core.pose) clearPoseExtraScores() (in module pyrosetta.rosetta.core.pose) clearSmallPockets() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) clockwise() (in module pyrosetta.rosetta.core.membrane) clone() (pyrosetta.rosetta.basic.datacache.CacheableData method) (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringIntegerMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) Clone() (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) clone() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphContainer method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AROMATIC method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.CHARGED method) (pyrosetta.rosetta.core.pack.task.EMPTY method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NC method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.PIKRNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PROPERTY method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.RESET method) (pyrosetta.rosetta.core.pack.task.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.DipolarCoupling method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.NeighborList method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.TotalEnergyMetric method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions method) (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringProtocol method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborsByDistanceCalculator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.NCSResMapping method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation method) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator method) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator method) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOptionKey method)

clone_as_base_class() (pyrosetta.rosetta.core.scoring.ScoreFunction method) clone_cache_data() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) clone_flipping_chirality() (pyrosetta.rosetta.core.conformation.Residue method) clone_info() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) clone_scorefxn() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) clone_shifted() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) clone_with_frags() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) clone_with_template() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) close() (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ozstream method) close_chainbreaks() (in module pyrosetta.rosetta.protocols.jumping) close_gaps() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) close_loops() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) close_one_loop_stem() (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) close_one_loop_stem_helper() (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) close_to_dna() (in module pyrosetta.rosetta.protocols.dna) CloseContactResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) closed_loop() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) CloseOneCDRLoop (class in pyrosetta.rosetta.protocols.antibody) CloseOneMover (class in pyrosetta.rosetta.protocols.antibody_legacy) closest_by_dist4() (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) closest_interface_residue() (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) closest_larger_peptide_vertex() (in module pyrosetta.rosetta.protocols.forge.methods) closest_orient_atoms_msd() (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) closest_smaller_peptide_vertex() (in module pyrosetta.rosetta.protocols.forge.methods) closest_suite() (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) closure_fragments() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) ClosureProblem (class in pyrosetta.rosetta.protocols.kinematic_closure) ClosureSolution (class in pyrosetta.rosetta.protocols.kinematic_closure) CloudPDBWriter (class in pyrosetta.rosetta.protocols.match.output) cluster() (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.cluster.APCluster method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) cluster_by_all_atom_rmsd() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) Cluster_Member (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) cluster_results() (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) cluster_rmsd() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) cluster_sampling_cutoff() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) cluster_sites() (in module pyrosetta.rosetta.core.pack) clusterCPockets() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) ClusterData (class in pyrosetta.rosetta.protocols.antibody.clusters) clustered_pose_list() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) clusterPockets() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) ClusterPoseSelector (class in pyrosetta.rosetta.protocols.pose_selectors) cm_main() (in module pyrosetta.rosetta.protocols.comparative_modeling) cmd() (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) cmdline_options_activated() (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) CoarseRNA_Fragments (class in pyrosetta.rosetta.protocols.rna.denovo.coarse) CoarseRNA_LoopCloser (class in pyrosetta.rosetta.protocols.rna.denovo.coarse) code() (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) code_from_6bit() (in module pyrosetta.rosetta.utility) code_to_6bit() (in module pyrosetta.rosetta.utility) codon2aa() (in module pyrosetta.rosetta.core.chemical.NucleotideTools) collapse() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) collect_all_inverse_rotamers() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) ColorMode (class in pyrosetta.rosetta.protocols.viewer.graphics_states_param) com() (in module pyrosetta.rosetta.protocols.membrane) combine_and_trim() (in module pyrosetta.rosetta.protocols.nonlocal) combine_constraints() (in module pyrosetta.rosetta.core.scoring.constraints) combine_long_loop_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) combine_movemaps_post_insertion() (in module pyrosetta.rosetta.protocols.grafting) combine_names() (in module pyrosetta.rosetta.utility.file) combine_residue_selections() (pyrosetta.rosetta.core.select.residue_selector.SSElementSelector method) combine_sequence_mappings() (in module pyrosetta.rosetta.core.id) Combine_Tags_Info (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna) combine_two_poses() (in module pyrosetta.rosetta.protocols.seeded_abinitio) CombinedConstraintEvaluatorCreator (class in pyrosetta.rosetta.protocols.constraints_additional) CombinedFilter (class in pyrosetta.rosetta.protocols.filters) command_string() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) comment_begin() (in module pyrosetta.rosetta.core.pack.task) comment_exists() (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) comment_from_line() (pyrosetta.rosetta.core.io.silent.SilentStruct method) comment_line() (pyrosetta.rosetta.core.io.silent.SilentFileData method) comment_lines() (pyrosetta.rosetta.core.io.silent.SilentFileData method) comment_name() (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) comment_value() (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) commit_change() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) commit_considered_substitution() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) common_type() (pyrosetta.rosetta.utility.tag.XMLSchemaType method) comparable() (in module pyrosetta.rosetta.utility.keys) compare_atom_coordinates() (in module pyrosetta.rosetta.core.pose) compare_binary_protein_silent_struct() (in module pyrosetta.rosetta.core.pose) compare_by_x (class in pyrosetta.rosetta.protocols.hbnet) compare_motif2scaffold_data_by_scaffold_low2high() (in module pyrosetta.rosetta.protocols.motif_grafting.movers) compare_RNA_char() (in module pyrosetta.rosetta.core.import_pose) compare_RNA_secstruct() (in module pyrosetta.rosetta.core.import_pose) compare_to_native() (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison method) compare_to_ref() (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) CompareByScoreCombination (class in pyrosetta.rosetta.protocols.frag_picker) compareCoverage() (pyrosetta.rosetta.protocols.pockets.ComparisonGrid method) CompareQueryPosition (class in pyrosetta.rosetta.protocols.frag_picker) CompareScoreComponent (class in pyrosetta.rosetta.protocols.frag_picker) CompareTotalScore (class in pyrosetta.rosetta.protocols.frag_picker) comparison_type (class in pyrosetta.rosetta.protocols.simple_filters) ComparisonGrid (class in pyrosetta.rosetta.protocols.pockets) compatibility_check() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) compatible_restype() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) compatible_with() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) completed() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) completed_job_summary() (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) CompletedJobOutput (class in pyrosetta.rosetta.protocols.jd3) complex_ring_detection() (in module pyrosetta.rosetta.core.chemical) complex_type_generator_for_anchored_graft_mover() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) complex_type_generator_for_backbone_mover() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) complex_type_generator_for_logical_selector() (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) complex_type_generator_for_loop_protocol() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) complex_type_generator_for_min_mover() (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) complex_type_generator_for_pack_pwat_rotamers_mover() (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) complex_type_generator_for_pack_rotamers_mover() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) complex_type_generator_for_rotamer_trials_mover() (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) complex_type_name_for_architect() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) complex_type_name_for_cluster_metric() (in module pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster) complex_type_name_for_features_reporter() (in module pyrosetta.rosetta.protocols.features) complex_type_name_for_filter() (in module pyrosetta.rosetta.protocols.filters) complex_type_name_for_jump_selector() (in module pyrosetta.rosetta.core.select.jump_selector) complex_type_name_for_loader() (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) complex_type_name_for_locator() (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) complex_type_name_for_loop_definer() (in module pyrosetta.rosetta.protocols.loops.loops_definers) complex_type_name_for_mover() (in module pyrosetta.rosetta.protocols.moves) complex_type_name_for_res_filter() (in module pyrosetta.rosetta.core.pack.task.operation) complex_type_name_for_res_lvl_task_op() (in module pyrosetta.rosetta.core.pack.task.operation) complex_type_name_for_residue_selector() (in module pyrosetta.rosetta.core.select.residue_selector) complex_type_name_for_scoring_grid() (in module pyrosetta.rosetta.protocols.qsar.scoring_grid) complex_type_name_for_simple_metric() (in module pyrosetta.rosetta.core.simple_metrics) complex_type_name_for_task_op() (in module pyrosetta.rosetta.core.pack.task.operation) complex_typename_for_element() (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) CompositeEnergyMetric (class in pyrosetta.rosetta.protocols.analysis.simple_metrics) CompositeFragmentSelector (class in pyrosetta.rosetta.protocols.frag_picker) CompositeRealMetric (class in pyrosetta.rosetta.core.simple_metrics) CompositeStringMetric (class in pyrosetta.rosetta.core.simple_metrics) compound_in_progress() (pyrosetta.rosetta.core.io.HeaderInformation method) compound_token_to_string() (pyrosetta.rosetta.core.io.HeaderInformation method) CompoundArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) CompoundFilter (class in pyrosetta.rosetta.protocols.filters) CompoundPerturber (class in pyrosetta.rosetta.protocols.denovo_design.components) compounds() (pyrosetta.rosetta.core.io.HeaderInformation method) compress() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) compressed() (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) compute() (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator method) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator method) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator method) compute_alt_weights_for_npd_hbonds() (in module pyrosetta.rosetta.core.pack.interaction_graph) compute_atom_packing_scores() (in module pyrosetta.rosetta.core.scoring.packstat) compute_avge_scores() (in module pyrosetta.rosetta.protocols.sasa_scores) compute_bb_centroid() (in module pyrosetta.rosetta.core.scoring) compute_bb_radius() (in module pyrosetta.rosetta.core.scoring) compute_cav_ball_neighbor_count() (in module pyrosetta.rosetta.core.scoring.packstat) compute_cav_ball_volumes() (in module pyrosetta.rosetta.core.scoring.packstat) compute_center_of_mass() (in module pyrosetta.rosetta.protocols.forge.remodel) compute_centroid_environment() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) compute_csascore() (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) compute_dcentroid_environment() (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) compute_dcscore() (pyrosetta.rosetta.core.scoring.DipolarCoupling method) compute_dec15_score() (in module pyrosetta.rosetta.core.scoring.packing) compute_designable_neighbors() (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) compute_dipscore() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) compute_dipscore_nls() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) compute_dipscore_nlsDa() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) compute_dipscore_nlsDaR() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) compute_dipscore_nlsR() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) compute_embeddings_by_chain() (in module pyrosetta.rosetta.protocols.membrane) compute_exact_geosol() (in module pyrosetta.rosetta.core.scoring.geometric_solvation) compute_fa_projection() (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) compute_folding_energies() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) compute_func() (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) compute_holes_deriv() (in module pyrosetta.rosetta.core.scoring.packing) compute_holes_deriv_res() (in module pyrosetta.rosetta.core.scoring.packing) compute_holes_score() (in module pyrosetta.rosetta.core.scoring.packing) compute_holes_score_res() (in module pyrosetta.rosetta.core.scoring.packing) compute_interface() (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) compute_matching_energy() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential method) compute_membrane_embedding() (pyrosetta.rosetta.core.scoring.MembranePotential method) compute_mpair_score() (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) compute_mpcbeta_score() (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) compute_mpenv_score() (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) compute_nonhelix_penalty() (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) compute_nres_in_asymmetric_unit() (in module pyrosetta.rosetta.protocols.constraint_generator) compute_one_and_two_body_energies() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) compute_one_body_energies() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) compute_one_body_energy_maps() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) compute_packing_score() (in module pyrosetta.rosetta.core.scoring.packstat) compute_packing_score_leerichards() (in module pyrosetta.rosetta.core.scoring.packstat) compute_pairwise_score() (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) compute_penalty() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) compute_per_residue_coverage() (in module pyrosetta.rosetta.core.fragment) compute_pose_hpatch_score() (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) compute_pose_surface_energy() (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) compute_proposal_density() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) compute_proton_chi_samplings() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) compute_residue_packing_score() (in module pyrosetta.rosetta.core.scoring.packstat) compute_residue_packing_scores() (in module pyrosetta.rosetta.core.scoring.packstat) compute_residue_sasas_for_sasa_scores() (in module pyrosetta.rosetta.protocols.sasa_scores) compute_residue_surface_energy() (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) compute_rosettaholes_score() (in module pyrosetta.rosetta.core.scoring.packing) compute_rotdensities() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) compute_sasa() (in module pyrosetta.rosetta.core.scoring.packstat) compute_sasapack_scores() (in module pyrosetta.rosetta.protocols.sasa_scores) compute_sc_centroid() (in module pyrosetta.rosetta.core.scoring) compute_sc_radius() (in module pyrosetta.rosetta.core.scoring) compute_size() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) compute_ss_regions() (in module pyrosetta.rosetta.protocols.loops) compute_structure_based_embedding() (in module pyrosetta.rosetta.protocols.membrane) compute_surface_area_leerichards() (in module pyrosetta.rosetta.core.scoring.packstat) compute_surface_area_leerichards_deriv() (in module pyrosetta.rosetta.core.scoring.packstat) compute_surrounding_sasa() (in module pyrosetta.rosetta.core.scoring.packstat) compute_tensor_stats() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) compute_termini_penalty() (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) compute_tmproj_penalty() (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) compute_total_score() (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) compute_total_volume_of_current_residues() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) compute_unique_chains() (in module pyrosetta.rosetta.core.pose) compute_unsats_all_nodes() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) compute_unsats_changed_nodes() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) compute_unsats_for_node() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) compute_volume_of_this_buried_rotamer() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) concave_shell() (in module pyrosetta.rosetta.core.membrane) concavity_direction() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) concavity_reference_residue() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) ConcurrencyTestCreator (class in pyrosetta.rosetta.protocols.features.helixAssembly) cond_exit() (in module pyrosetta.rosetta.utility) conditional_erase() (pyrosetta.rosetta.core.pose.PDBPoseMap method) conf2pdb_chain() (in module pyrosetta.rosetta.core.pose) conf_size() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) confidence() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) configure_hbond_options() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) configure_rotameric_single_residue_dunbrack_library() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser method) Conformation (class in pyrosetta.rosetta.core.conformation) conformation() (pyrosetta.rosetta.core.pose.Pose method) conformation_ptr() (pyrosetta.rosetta.core.pose.Pose method) ConformationEvent (class in pyrosetta.rosetta.core.pose.signals) conformer_found() (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) conformers_for_ring_size() (pyrosetta.rosetta.core.chemical.rings.RingConformerManager method) ConformerSwitchMover (class in pyrosetta.rosetta.protocols.docking) conj_map_times() (in module pyrosetta.rosetta.core.scoring.electron_density) conjugability() (pyrosetta.rosetta.core.chemical.Bond method) connect_atom() (pyrosetta.rosetta.core.conformation.Residue method) connect_info_cutoff() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) connect_map() (pyrosetta.rosetta.core.conformation.Residue method) connect_map_size() (pyrosetta.rosetta.core.conformation.Residue method) connected() (pyrosetta.rosetta.core.kinematics.FoldTree method) connected_by_twobonds() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) connected_residue_at_lower() (pyrosetta.rosetta.core.conformation.Residue method) connected_residue_at_resconn() (pyrosetta.rosetta.core.conformation.Residue method) connected_residue_at_upper() (pyrosetta.rosetta.core.conformation.Residue method) connected_resonance_ids() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) connected_resonances() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) connection_distance() (pyrosetta.rosetta.core.conformation.Residue method) connection_incomplete() (pyrosetta.rosetta.core.conformation.Residue method) ConnectionArchitect (class in pyrosetta.rosetta.protocols.denovo_design.connection) ConnectionEvent (class in pyrosetta.rosetta.core.conformation.signals) ConnectionEvent.Tag (class in pyrosetta.rosetta.core.conformation.signals) ConnectionPerturber (class in pyrosetta.rosetta.protocols.denovo_design.components) connections_match() (pyrosetta.rosetta.core.conformation.Residue method) connections_to_residue() (pyrosetta.rosetta.core.conformation.Residue method) connectivity_index() (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) ConnectRight (class in pyrosetta.rosetta.protocols.forge.build) ConnectSulfurAndMakeVirtualProton (class in pyrosetta.rosetta.core.chemical) connid() (pyrosetta.rosetta.core.chemical.ResConnID method) ConsensusDesignMover (class in pyrosetta.rosetta.protocols.calc_taskop_movers) ConsensusSequenceType (class in pyrosetta.rosetta.core.enzymes) conservation_cutoff_aligned_segments() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) conservation_cutoff_protein_interface_design() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) ConservativeDesignOperation (class in pyrosetta.rosetta.protocols.task_operations) consider_mainchain_only() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) consider_substitution() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) const_access_Real_MathNTensor() (in module pyrosetta.rosetta.numeric) const_begin() (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) const_data_cache() (pyrosetta.rosetta.core.pose.Pose method) const_data_map() (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) const_edge() (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) const_edge_list_begin() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) const_edge_list_end() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) const_end() (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) const_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) const_last() (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) const_lower_edge_list_begin() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) const_lower_edge_list_end() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) const_my_group() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) const_neighbor_iterator_begin() (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) const_neighbor_iterator_end() (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) const_next() (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) const_pose_apply() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) const_previous() (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) const_residues() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) const_upper_edge_list_begin() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) const_upper_edge_list_end() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) const_upper_neighbor_iterator_begin() (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) const_upper_neighbor_iterator_end() (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) const_vdw_cached_rep_screen_info_from_pose() (in module pyrosetta.rosetta.protocols.scoring) constant() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) ConstantConstraint (class in pyrosetta.rosetta.core.scoring.constraints) ConstantFunc (class in pyrosetta.rosetta.core.scoring.func) ConstantLengthFragSet (class in pyrosetta.rosetta.core.fragment) ConstDataMap (class in pyrosetta.rosetta.basic.datacache) constrain_coords() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) constrain_ligand_torsions() (in module pyrosetta.rosetta.protocols.ligand_docking) constrain_linker() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) constrain_pose_res_to_invrots() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) constrain_relax_segments() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) constrain_relax_to_native_coords() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) constrain_relax_to_start_coords() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) constrain_residue() (in module pyrosetta.rosetta.protocols.mpi_refinement) constrain_ring_atoms() (in module pyrosetta.rosetta.core.pose.ncbb) constrain_to_antigen_chains() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) constrain_to_epitope_residues() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) constrain_to_paratope_cdrs() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) constrain_to_paratope_residues() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) ConstrainHBondNetwork (class in pyrosetta.rosetta.protocols.hbnet) Constraint (class in pyrosetta.rosetta.core.scoring.constraints) constraint_set() (pyrosetta.rosetta.core.pose.Pose method) constraint_set_slice() (in module pyrosetta.rosetta.protocols.stepwise.modeler) ConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) ConstraintEvaluatorCreator (class in pyrosetta.rosetta.protocols.constraints_additional) ConstraintEvaluatorWrapperCreator (class in pyrosetta.rosetta.protocols.topology_broker) ConstraintFragmentSampler (class in pyrosetta.rosetta.protocols.abinitio) ConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) ConstraintGeneratorLoader (class in pyrosetta.rosetta.protocols.parser) ConstraintIO (class in pyrosetta.rosetta.core.scoring.constraints) ConstrainToIdealMover (class in pyrosetta.rosetta.protocols.simple_moves) constraints() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) constraints_from_link_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) constraints_NtoC() (in module pyrosetta.rosetta.protocols.flxbb) constraints_only() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) constraints_sheet() (in module pyrosetta.rosetta.protocols.flxbb) ConstraintScoreFilter (class in pyrosetta.rosetta.protocols.constraint_filters) ConstraintSet (class in pyrosetta.rosetta.core.scoring.constraints) ConstraintsManager (class in pyrosetta.rosetta.protocols.constraint_generator) ConstraintsMap (class in pyrosetta.rosetta.protocols.constraint_generator) construct_and_dump_outpose() (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination method) construct_dummy_pose() (in module pyrosetta.rosetta.protocols.denovo_design) construct_from_pose() (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) construct_kd_tree() (in module pyrosetta.rosetta.numeric.kdtree) construct_poly_ala_pose() (in module pyrosetta.rosetta.protocols.denovo_design) (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) construct_poly_beta_ala_pose() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) construct_poly_d_ala_pose() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) construct_poly_d_beta_ala_pose() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) construct_poly_uniq_restype_pose() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) construct_poly_XXX_pose() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) ConstScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) Contact (class in pyrosetta.rosetta.protocols.contact_map) contact_distance2() (in module pyrosetta.rosetta.protocols.dna) contact_name() (in module pyrosetta.rosetta.protocols.frag_picker) contact_order() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) contact_type() (in module pyrosetta.rosetta.protocols.frag_picker) ContactMapEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) ContactPartner (class in pyrosetta.rosetta.protocols.contact_map) ContactType (class in pyrosetta.rosetta.protocols.frag_picker) contain() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) contain_nic() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) contains() (in module pyrosetta.rosetta.protocols.hbnet) (in module pyrosetta.rosetta.protocols.sparta) Contains() (in module pyrosetta.rosetta.protocols.toolbox) contains() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.forge.build.Interval method) contains_atom_type() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) contains_bond_length() (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) contains_carbohydrate_residues() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) contains_element_type() (pyrosetta.rosetta.core.chemical.ElementSet method) contains_position() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) contains_protein() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) contains_seqpos() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) context_derivative_empty() (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) context_graph() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) ContextGraphType (class in pyrosetta.rosetta.core.scoring) continue_if_silent() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) continuous() (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) ContinuousAssembly (class in pyrosetta.rosetta.protocols.legacy_sewing) controlling_chi_for_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) ControlStrength (class in pyrosetta.rosetta.protocols.environment.claims) conventional_chains() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) conventional_numbering() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) converge() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) ConvergenceTest (class in pyrosetta.rosetta.core.optimization) convert_aa_to_index() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPairDistPotential method) convert_acgu_to_1234() (in module pyrosetta.rosetta.core.chemical.rna) convert_atom_name() (in module pyrosetta.rosetta.core.io.pose_from_sfr) convert_based_on_match_type() (in module pyrosetta.rosetta.core.import_pose) convert_binary_checkpoint() (in module pyrosetta.rosetta.protocols.frag_picker) convert_cartesian_to_grid() (in module pyrosetta.rosetta.protocols.pockets) convert_cartesian_to_spherical_coor_triplet() (in module pyrosetta.rosetta.protocols.pockets) convert_from_std_map() (in module pyrosetta.rosetta.core.pose) convert_GeomSampleInfo_to_FuncOP() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) convert_grid_to_cartesian() (in module pyrosetta.rosetta.protocols.pockets) convert_inorder_table_to_original_order() (in module pyrosetta.rosetta.core.scoring.trie) convert_inorder_vector_to_original_order() (in module pyrosetta.rosetta.core.scoring.trie) convert_res_name() (in module pyrosetta.rosetta.core.io.pose_from_sfr) convert_residue_names_into_linkage_map_key() (in module pyrosetta.rosetta.core.chemical.carbohydrates) convert_scores_to_probabilities() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) convert_spherical_coor_triplet_to_cartesian() (in module pyrosetta.rosetta.protocols.pockets) convert_sugar_modeling_to_residue_alternative_set() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) convert_to_BondName() (in module pyrosetta.rosetta.core.chemical) convert_to_fasta() (in module pyrosetta.rosetta.core.sequence) convert_to_working_res() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) ConvertRealToVirtualMover (class in pyrosetta.rosetta.protocols.simple_moves) ConvertVirtualToRealMover (class in pyrosetta.rosetta.protocols.simple_moves) convolute_maps() (in module pyrosetta.rosetta.core.scoring.electron_density) coord() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) coord_constrain_sidechains() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) coord_frame_ref() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) coordinate_constrain_selection() (in module pyrosetta.rosetta.protocols.relax) coordinate_constraint_weight() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) coordinate_constraints_during_minimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) coordinate_for_nonchi_atom_in_ideal_frame() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) CoordinateConstraint (class in pyrosetta.rosetta.core.scoring.constraints) CoordinateConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) CoordinateConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) coordinates() (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) coords() (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.protocols.toolbox.KClusterData method) copy() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) copy_all_o2prime_torsions() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) copy_bb_donor_acceptor_arrays() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) copy_bulge_res_and_sugar_torsion() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) copy_clone() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) copy_connectivity() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) copy_coords() (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) copy_data() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) copy_dna_chains() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) copy_dofs() (in module pyrosetta.rosetta.core.pose.copydofs) copy_dofs_from_pose() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) copy_dofs_match_atom_names() (in module pyrosetta.rosetta.core.pose.copydofs) copy_dofs_sort_criterion() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) copy_dofs_to_pose() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) copy_fragments() (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) copy_from() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) copy_helix_bondangles() (in module pyrosetta.rosetta.protocols.helical_bundle) copy_helix_bondlengths() (in module pyrosetta.rosetta.protocols.helical_bundle) copy_helix_dihedrals() (in module pyrosetta.rosetta.protocols.helical_bundle) copy_loop_pose_to_original() (in module pyrosetta.rosetta.protocols.generalized_kinematic_closure) copy_next_pose_segment() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) copy_node_and_connected_edges() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) copy_over_phosphate_variants() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) copy_pdbinfo() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) copy_pose_crd() (in module pyrosetta.rosetta.protocols.mpi_refinement) copy_residue_connections() (pyrosetta.rosetta.core.conformation.Residue method) copy_residue_connections_from() (pyrosetta.rosetta.core.conformation.Residue method) copy_residue_coordinates_and_rebuild_missing_atoms() (in module pyrosetta.rosetta.core.conformation) copy_scores() (pyrosetta.rosetta.core.io.silent.SilentStruct method) copy_segment() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) copy_targeted_dna() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) copy_values() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) copy_without_output() (pyrosetta.rosetta.protocols.jd2.Job method) CopyRotamerMover (class in pyrosetta.rosetta.protocols.simple_moves) copysign() (in module pyrosetta.rosetta.utility) COradius2() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) corrcoef() (in module pyrosetta.rosetta.numeric.statistics) corrcoef_with_provided_mean_and_std_dev() (in module pyrosetta.rosetta.numeric.statistics) correct_polymer_dependent_atoms_in_pose_segment() (in module pyrosetta.rosetta.protocols.generalized_kinematic_closure) correctly_add_cutpoint_variants() (in module pyrosetta.rosetta.core.pose) correctly_remove_variants_incompatible_with_lower_cutpoint_variant() (in module pyrosetta.rosetta.core.pose) correctly_remove_variants_incompatible_with_upper_cutpoint_variant() (in module pyrosetta.rosetta.core.pose) corresponding_res_block() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) corresponding_residue_in_current() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) cos_theta() (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) COSFXN() (in module pyrosetta.rosetta.numeric.crick_equations) could_be_accepted() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) CouldHaveHybridization() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) count() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.numeric.model_quality.RmsData method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) count_AA_w_direction() (in module pyrosetta.rosetta.protocols.features.strand_assembly) count_AA_wo_direction() (in module pyrosetta.rosetta.protocols.features.strand_assembly) count_accepted() (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) count_bb_atoms() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) count_bb_atoms_in_residue() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) count_bulges() (in module pyrosetta.rosetta.protocols.denovo_design) count_candidates() (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) count_CBs() (in module pyrosetta.rosetta.protocols.sic_dock) count_components() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) count_connected_components_and_initialize_vertex_groups() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) count_cutpoints() (in module pyrosetta.rosetta.protocols.forge.methods) count_dynamic_memory() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) count_energy_drop() (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) count_ff() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) count_fixed_residues() (pyrosetta.rosetta.core.kinematics.FoldTree method) count_gly_as_polar() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) count_linkers() (in module pyrosetta.rosetta.protocols.sic_dock) count_n_matches() (pyrosetta.rosetta.protocols.match.MatchCounter method) count_num_covered() (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) count_pair_hybrid() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) count_pools() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) count_query_ss() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) count_selected() (in module pyrosetta.rosetta.core.select.residue_selector) count_static_memory() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) count_trial() (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) count_uniq_char() (in module pyrosetta.rosetta.protocols.ncbb) counted_residue_description() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) CountFromLeft (class in pyrosetta.rosetta.protocols.forge.build) CountPairRepMap (class in pyrosetta.rosetta.core.scoring.elec) counts() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) CoupledMover (class in pyrosetta.rosetta.protocols.simple_moves) cov() (in module pyrosetta.rosetta.numeric.statistics) cov_with_provided_mean() (in module pyrosetta.rosetta.numeric.statistics) covalent_compliance() (in module pyrosetta.rosetta.protocols.noesy_assign) CovalentCompliance (class in pyrosetta.rosetta.protocols.noesy_assign) CovalentConnectionReplaceInfo (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) CovalentResidueNetwork (class in pyrosetta.rosetta.protocols.toolbox) CPCrossoverBehavior (class in pyrosetta.rosetta.core.scoring.etable.count_pair) CPParameter (class in pyrosetta.rosetta.core.chemical.rings) CPResidueConnectionType (class in pyrosetta.rosetta.core.scoring.etable.count_pair) crankshaft_alpha_gamma() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) create() (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) create_acc_orientation_vector() (in module pyrosetta.rosetta.core.scoring.hbonds) create_alignment_id_map_legacy() (in module pyrosetta.rosetta.protocols.stepwise.modeler.align) create_alpha_beta_models_table() (in module pyrosetta.rosetta.protocols.legacy_sewing) create_and_init_atom_level_hbond_graph() (in module pyrosetta.rosetta.core.pack.hbonds) create_assembly() (pyrosetta.rosetta.protocols.legacy_sewing.AssemblyFactory method) create_atom_tree() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) create_blank_file() (in module pyrosetta.rosetta.utility.file) create_bond_length() (in module pyrosetta.rosetta.core.chemical) create_cache() (in module pyrosetta.rosetta.protocols.frag_picker.scores) create_chimera_segment() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) create_command_map() (in module pyrosetta.rosetta.core.pack.task) create_comparer() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator method) create_complex_type_generator() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) create_consensus_design_task() (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) create_constraint() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator method) create_cpdata_correspondence_for_rotamer() (in module pyrosetta.rosetta.core.scoring.trie) create_cpdata_correspondence_for_rotamerset() (in module pyrosetta.rosetta.core.scoring.trie) create_data() (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator method) create_directed_dependency() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) create_directory() (in module pyrosetta.rosetta.utility.file) create_directory_recursive() (in module pyrosetta.rosetta.utility.file) create_docking_high_res_mover() (pyrosetta.rosetta.protocols.docking.DockingHighResFactory method) create_don_orientation_vector() (in module pyrosetta.rosetta.core.scoring.hbonds) create_empty_map() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) create_energy_method() (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator method) create_entity_resfile_contents() (in module pyrosetta.rosetta.protocols.pack_daemon) create_euler_rotation() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) create_ExactSHOEnergy_from_cmdline() (in module pyrosetta.rosetta.core.scoring.geometric_solvation) create_expression_tree() (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) create_extra_output() (in module pyrosetta.rosetta.protocols.floppy_tail) create_fasta_file() (in module pyrosetta.rosetta.core.sequence) create_features_reporter() (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator method) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator method) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator method) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator method) create_filter() (pyrosetta.rosetta.protocols.filters.FilterCreator method) create_fragment_set() (in module pyrosetta.rosetta.protocols.hybridization) create_fragment_set_no_ssbias() (in module pyrosetta.rosetta.protocols.hybridization) create_from_cacheable_data() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) create_from_motifs() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) create_from_pose() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) create_from_remarks() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) create_from_tag() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) create_from_xml() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) create_full_to_input_res_map() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) create_func() (in module pyrosetta.rosetta.protocols.constraint_generator) create_glycan_movemap_from_residue_selector() (in module pyrosetta.rosetta.core.pose.carbohydrates) create_grid() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator method) create_info() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) create_init_and_create_edges_for_atom_level_hbond_graph() (in module pyrosetta.rosetta.core.pack.hbonds) create_inner_cycle() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory method) create_instance() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) create_JobInputter() (pyrosetta.rosetta.protocols.jd2.JobInputterCreator method) create_JobOutputter() (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator method) create_jump_fragments() (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) create_jump_sample() (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) create_loader() (pyrosetta.rosetta.protocols.parser.DataLoaderCreator method) create_long_range_energy_container() (in module pyrosetta.rosetta.core.scoring.methods) create_loop_mover() (pyrosetta.rosetta.protocols.loops.LoopMoverFactory method) create_loops_definer() (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator method) create_match_position_modifier() (in module pyrosetta.rosetta.protocols.match) create_membrane_docking_foldtree_from_partners() (in module pyrosetta.rosetta.protocols.membrane) create_membrane_foldtree_anchor_com() (in module pyrosetta.rosetta.protocols.membrane) create_membrane_foldtree_anchor_pose_tmcom() (in module pyrosetta.rosetta.protocols.membrane) create_membrane_foldtree_anchor_tmcom() (in module pyrosetta.rosetta.protocols.membrane) create_membrane_foldtree_from_anchors() (in module pyrosetta.rosetta.protocols.membrane) create_membrane_multi_partner_foldtree_anchor_tmcom() (in module pyrosetta.rosetta.protocols.membrane) create_model_from_pose() (in module pyrosetta.rosetta.protocols.legacy_sewing) create_mover() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMoverCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraintCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraintCreator method) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator method) (pyrosetta.rosetta.protocols.moves.MoverCreator method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator method) create_new_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) create_new_node() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) create_new_parameters_set() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) create_oriented_water_rotamer() (in module pyrosetta.rosetta.core.pack.rotamer_set) create_output_specification() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter method) create_output_upstream_pose() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) create_packer_graph() (in module pyrosetta.rosetta.core.pack) create_packer_task() (pyrosetta.rosetta.core.pack.task.TaskFactory method) create_pdb_contents_from_sfr() (in module pyrosetta.rosetta.core.io.pdb) create_protocol() (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator method) create_rdf_function() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator method) create_remark_headers_from_cstcache() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) create_reporter() (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator method) create_requirement() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalRequirementCreator method) create_res_filter() (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator method) create_res_level_task_operation() (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) create_residue() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.ResidueFactory method) create_resource_loader() (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.core.fragment.FragmentSetLoaderCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator method) create_resource_locator() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator method) create_resource_manager_from_options_system() (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory method) create_rna_vall_torsions() (in module pyrosetta.rosetta.protocols.rna.denovo) create_rotamer() (pyrosetta.rosetta.core.conformation.Residue method) create_rotamer_string() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) create_sample_vector() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) create_sasa_method() (in module pyrosetta.rosetta.core.scoring.sasa) create_score_function() (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory method) create_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) create_scores() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) create_scoring_method() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) create_SecMatchResiduePairEvaluatorOP() (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory method) create_selector() (pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator method) create_sequence() (pyrosetta.rosetta.core.sequence.SequenceCreator method) create_sequence_profile_constraints() (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) create_sequons() (in module pyrosetta.rosetta.protocols.carbohydrates) create_sfr_from_cif_file_op() (in module pyrosetta.rosetta.core.io.mmcif) create_sfr_from_pdb_file_contents() (in module pyrosetta.rosetta.core.io.pdb) create_shuffle_map_recursive_rms() (in module pyrosetta.rosetta.core.scoring) create_silent_struct() (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.SilentStructCreator method) create_SilentStructOP() (pyrosetta.rosetta.core.io.silent.SilentFileData method) create_specific_membrane_foldtree() (in module pyrosetta.rosetta.protocols.membrane) create_standard_o2prime_pack_task() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) create_subpose() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) create_surface_params() (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader method) create_tag() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) create_tag_from_xml() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) create_tag_from_xml_string() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) create_task_and_apply_taskoperations() (pyrosetta.rosetta.core.pack.task.TaskFactory method) create_task_for_allhotspot_packing() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) create_task_for_hotspot_packing() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) create_task_operation() (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator method) create_temp_filename() (in module pyrosetta.rosetta.utility.file) create_torsion_value_string() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) create_working_data() (in module pyrosetta.rosetta.core.io.pose_from_sfr) CreateGlycanSequonMover (class in pyrosetta.rosetta.protocols.carbohydrates) creates_undefined_backbone() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) CreateSequenceMotifMover (class in pyrosetta.rosetta.protocols.calc_taskop_movers) cross() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.numeric.kinematic_closure) CrossLinker (class in pyrosetta.rosetta.protocols.cyclic_peptide) CrosslinkerMover (class in pyrosetta.rosetta.protocols.cyclic_peptide) CrosslinkerMoverHelper (class in pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) crossover() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) crossover_ft() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) crosspeak() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) CrossPeakInfo (class in pyrosetta.rosetta.protocols.noesy_assign) crosspeaks() (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) crystinfo() (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.pose.PDBInfo method) crystRMS() (in module pyrosetta.rosetta.protocols.cryst) crystRMSfast() (in module pyrosetta.rosetta.protocols.cryst) CSA (class in pyrosetta.rosetta.core.scoring) CSAcomputed() (pyrosetta.rosetta.core.scoring.CSA method) CSAerr() (pyrosetta.rosetta.core.scoring.CSA method) CSAval() (pyrosetta.rosetta.core.scoring.CSA method) CSI_bgBlack() (in module pyrosetta.rosetta.utility) CSI_bgBlue() (in module pyrosetta.rosetta.utility) CSI_bgCyan() (in module pyrosetta.rosetta.utility) CSI_bgDefault() (in module pyrosetta.rosetta.utility) CSI_bgGreen() (in module pyrosetta.rosetta.utility) CSI_bgMagenta() (in module pyrosetta.rosetta.utility) CSI_bgRed() (in module pyrosetta.rosetta.utility) CSI_bgWhite() (in module pyrosetta.rosetta.utility) CSI_bgYellow() (in module pyrosetta.rosetta.utility) CSI_Black() (in module pyrosetta.rosetta.utility) CSI_Blue() (in module pyrosetta.rosetta.utility) CSI_Bold() (in module pyrosetta.rosetta.utility) CSI_Cyan() (in module pyrosetta.rosetta.utility) CSI_Default() (in module pyrosetta.rosetta.utility) CSI_Enum (class in pyrosetta.rosetta.utility.CSI) CSI_Green() (in module pyrosetta.rosetta.utility) CSI_Magenta() (in module pyrosetta.rosetta.utility) CSI_Nothing() (in module pyrosetta.rosetta.utility) CSI_Red() (in module pyrosetta.rosetta.utility) CSI_Reset() (in module pyrosetta.rosetta.utility) CSI_Sequence (class in pyrosetta.rosetta.utility) CSI_Underline() (in module pyrosetta.rosetta.utility) CSI_White() (in module pyrosetta.rosetta.utility) CSI_Yellow() (in module pyrosetta.rosetta.utility) CSScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) cst_block() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) cst_file() (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) cst_gen_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader method) cst_io() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) cst_max_seq_sep() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) cst_residue_in_pose() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) cst_type() (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) CstAction (class in pyrosetta.rosetta.protocols.enzdes) cstAtoms() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) cstAtoms_defined() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) cstfile() (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) cstfile_name() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) CstInfoMover (class in pyrosetta.rosetta.protocols.constraint_movers) Cstring (class in pyrosetta.rosetta.ObjexxFCL) cstType (class in pyrosetta.rosetta.protocols.jumping) cterm_included() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) CTGenSubelementBehavior (class in pyrosetta.rosetta.utility.tag) cube() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.ObjexxFCL) cubic_interpolation() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) cubic_polynomial_deriv() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) cubic_polynomial_from_spline() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) cubic_roots1() (in module pyrosetta.rosetta.protocols.cluster.calibur) cubic_roots2() (in module pyrosetta.rosetta.protocols.cluster.calibur) cull_violators() (in module pyrosetta.rosetta.core.scoring.constraints) cumulate_jobs() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) cumulate_replicas() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) curr_num_in_recent_history() (pyrosetta.rosetta.utility.recent_history_queue method) curr_rot() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) current_acceptance_ratio() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) current_batch() (in module pyrosetta.rosetta.protocols.jd2) current_batch_id() (in module pyrosetta.rosetta.protocols.jd2) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) current_input_tag() (in module pyrosetta.rosetta.protocols.jd2) current_job() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) current_job_id() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) current_nstruct_index() (in module pyrosetta.rosetta.protocols.jd2) current_output_filename() (in module pyrosetta.rosetta.protocols.jd2) current_output_name() (in module pyrosetta.rosetta.protocols.jd2) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) current_replica() (in module pyrosetta.rosetta.protocols.jd2) current_rotamer() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) current_score() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) current_scorefxn() (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) current_size() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) current_trial() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) custom_angle() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) custom_rama_table() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) custom_type_name() (pyrosetta.rosetta.utility.tag.XMLSchemaType method) custom_variant_types() (pyrosetta.rosetta.core.chemical.ResidueType method) CustomScoreSelector (class in pyrosetta.rosetta.protocols.frag_picker) cut() (pyrosetta.rosetta.protocols.loops.Loop method) cut_bond() (pyrosetta.rosetta.core.chemical.Bond method) cut_bond_neighbor() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) cut_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) cut_residue() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) CutChainMover (class in pyrosetta.rosetta.protocols.simple_moves) cutoff() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) cutoff_buried_surface_area() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) cutoff_distance() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) cutpoint() (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) cutpoint_by_jump() (pyrosetta.rosetta.core.kinematics.FoldTree method) cutpoint_map() (pyrosetta.rosetta.core.kinematics.FoldTree method) cutpoint_open_in_full_model() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) cutpoint_probabilities() (in module pyrosetta.rosetta.protocols.medal) cutpoint_segment() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) cutpoint_separation() (in module pyrosetta.rosetta.protocols.antibody) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) cutpoints() (pyrosetta.rosetta.core.kinematics.FoldTree method) cutpoints_separation() (in module pyrosetta.rosetta.protocols.antibody) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) cutpos_list() (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) cwd() (in module pyrosetta.rosetta.utility.file) CycleMover (class in pyrosetta.rosetta.protocols.moves) cycles() (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) CyclicMover (class in pyrosetta.rosetta.protocols.moves) CyclizationMethod (class in pyrosetta.rosetta.protocols.peptide_deriver) CyclizationMover (class in pyrosetta.rosetta.protocols.simple_moves) cyclize_pose() (in module pyrosetta.rosetta.protocols.relax) cyclize_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) CycpepSymmetryFilter (class in pyrosetta.rosetta.protocols.cyclic_peptide)

D

d() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) d1() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) d2() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) d2s() (pyrosetta.rosetta.utility.subset_mapping method) d_array_scale() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) d_hbond_weight_dE() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) DaemonSetMessage (class in pyrosetta.rosetta.protocols.pack_daemon) data() (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) data_dim() (in module pyrosetta.rosetta.protocols.recces) data_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.DataLoaderFactory method) data_ptr() (pyrosetta.rosetta.core.conformation.Residue method) database_dir() (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepLibrary method) database_directory() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) database_fname() (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) database_mode_from_name() (in module pyrosetta.rosetta.utility.sql_database) database_session_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.DatabaseSessionLoader method) DatabaseJobInputter (class in pyrosetta.rosetta.protocols.features) DatabaseJobOutputter (class in pyrosetta.rosetta.protocols.features) DatabaseResourceLocator (class in pyrosetta.rosetta.basic.resource_manager.locator) DatabaseResourceLocatorCreator (class in pyrosetta.rosetta.basic.resource_manager.locator) DatabaseSessionLoader (class in pyrosetta.rosetta.protocols.parser) DatabaseThread (class in pyrosetta.rosetta.protocols.task_operations) DataLoader (class in pyrosetta.rosetta.protocols.parser) DataLoaderCreator (class in pyrosetta.rosetta.protocols.parser) DataLoaderFactory (class in pyrosetta.rosetta.protocols.parser) DataMap (class in pyrosetta.rosetta.basic.datacache) DataPoint (class in pyrosetta.rosetta.protocols.cluster) datatype() (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) date() (in module pyrosetta.rosetta.ObjexxFCL) Dawson() (in module pyrosetta.rosetta.numeric.statistics) dB_dBdnmtr() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) dB_dBnmtr() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) db_partition_from_options() (in module pyrosetta.rosetta.basic.database) dBR_dG() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) DbTrajectoryRecorder (class in pyrosetta.rosetta.protocols.canonical_sampling) DbTrajectoryRecorderCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) DC (class in pyrosetta.rosetta.core.scoring) DC.DC_TYPE (class in pyrosetta.rosetta.core.scoring) DCcomputed() (pyrosetta.rosetta.core.scoring.DC method) DCerr() (pyrosetta.rosetta.core.scoring.DC method) Dconst() (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.RDC method) DCval() (pyrosetta.rosetta.core.scoring.DC method) dD_dv1() (in module pyrosetta.rosetta.protocols.pockets) dD_dv2() (in module pyrosetta.rosetta.protocols.pockets) dD_dv3() (in module pyrosetta.rosetta.protocols.pockets) dD_dv4() (in module pyrosetta.rosetta.protocols.pockets) dD_dv5() (in module pyrosetta.rosetta.protocols.pockets) dD_dv6() (in module pyrosetta.rosetta.protocols.pockets) ddG_main() (in module pyrosetta.rosetta.protocols) DdGFeaturesCreator (class in pyrosetta.rosetta.protocols.features) deactivate() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) deallocate_arraypoolelement() (pyrosetta.rosetta.core.scoring.EnergyGraph method) deallocation_msg_type (class in pyrosetta.rosetta.protocols.jd3.deallocation) debug() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) debug_dump_icoor() (pyrosetta.rosetta.core.chemical.ResidueType method) debug_dump_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) debug_pause() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) debug_residue_torsions() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) decide_is_d_aa() (pyrosetta.rosetta.core.io.NomenclatureManager method) decide_is_known_achiral() (pyrosetta.rosetta.core.io.NomenclatureManager method) decide_is_l_aa() (pyrosetta.rosetta.core.io.NomenclatureManager method) decide_read_from_binary() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) decide_to_keep_pose() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) declare_chemical_bond() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) declare_chemical_bonds_at_cutpoints() (in module pyrosetta.rosetta.protocols.stepwise.modeler) declare_cutpoint_chemical_bond() (in module pyrosetta.rosetta.core.pose) declare_minimization_over() (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) DeclareStructureDataCovalentBondMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) decode6bit() (in module pyrosetta.rosetta.utility) decode_32_to_24() (in module pyrosetta.rosetta.utility) decompose() (in module pyrosetta.rosetta.protocols.nonlocal) decoy_compatibility() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) decoy_tag() (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) decoys() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) decoys_returned() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) decrease_double_lazy_ig_memlimit() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) decrease_linmem_ig_history_size() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) decreasing() (pyrosetta.rosetta.protocols.loops.Loop method) decrement_counts() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) decrement_from_cached() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) decrement_reference_pose_mapping_after_seqpos() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) def() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) default_active() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) default_filename() (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) default_inactive() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) default_jump_atom() (in module pyrosetta.rosetta.core.chemical.rna) default_movemap_factory_attribute_name() (in module pyrosetta.rosetta.core.select.movemap) default_position_from_affix() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) default_rts() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) default_score_function() (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) default_size() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) default_stereochem_from_code() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) default_string() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) default_to() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) default_value() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) DefaultCubeHash (class in pyrosetta.rosetta.core.conformation) define_architect_group() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) define_chains() (in module pyrosetta.rosetta.core.import_pose) define_composition_schema() (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) define_features_reporter_xml_schema_group() (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) define_global_requirements_subelement() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory method) define_intra_segment_requirements_subelement() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory method) define_loop_definer_xml_schema() (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) define_loops() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) define_mainchain_atoms() (in module pyrosetta.rosetta.core.chemical) define_mg_water_map() (in module pyrosetta.rosetta.protocols.magnesium) define_pairing_group() (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) define_rdf_function_group() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) define_scorable_core_from_secondary_structure() (in module pyrosetta.rosetta.protocols.loops) define_start_window() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) define_valid_filter_name_enumeration() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) define_valid_perturber_name_enumeration() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) define_valid_selector_name_enumeration() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) defined_adducts() (pyrosetta.rosetta.core.chemical.ResidueType method) defined_positions() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) defines_custom_rama_prepro_map() (pyrosetta.rosetta.core.chemical.ResidueType method) defines_dof_derivatives() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) defines_high_order_terms() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) defines_intrares_dof_derivatives() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) defines_intrares_energy() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) defines_intrares_energy_for_residue() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) defines_residue_pair_energy() (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) defines_retry_limit() (pyrosetta.rosetta.protocols.jd3.LarvalJob method) defines_score_for_residue() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) defines_score_for_residue_pair() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) definite_terminal_root() (in module pyrosetta.rosetta.core.pose) defs2map() (in module pyrosetta.rosetta.protocols.motifs) defs2vector() (in module pyrosetta.rosetta.protocols.motifs) degrees() (in module pyrosetta.rosetta.numeric.conversions) delete_act_coord_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) delete_all_intragroup_edges() (in module pyrosetta.rosetta.utility.graph) delete_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) delete_atom_alias() (pyrosetta.rosetta.core.chemical.ResidueType method) delete_carbohydrate_branch() (in module pyrosetta.rosetta.core.pose.carbohydrates) delete_chain_ending() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) delete_child_proton() (pyrosetta.rosetta.core.chemical.ResidueType method) delete_comment() (in module pyrosetta.rosetta.core.pose) delete_contents_at_nread_limit() (pyrosetta.rosetta.utility.io.FileContentsMap method) delete_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) delete_edges_with_degree_zero() (in module pyrosetta.rosetta.core.pack.hbonds) delete_extra_vertices() (pyrosetta.rosetta.core.kinematics.FoldTree method) delete_file_contents() (pyrosetta.rosetta.utility.io.FileContentsMap method) delete_jump_and_intervening_cutpoint() (pyrosetta.rosetta.core.kinematics.FoldTree method) delete_leaf() (in module pyrosetta.rosetta.core.pose.carbohydrates) delete_loop() (pyrosetta.rosetta.protocols.loops.Loops method) delete_lower_padding() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) delete_metalbinding_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) delete_node() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) delete_non_protein_from_pose() (in module pyrosetta.rosetta.protocols.rna.denovo) delete_overhang_residues() (in module pyrosetta.rosetta.protocols.grafting) delete_polymer_residue() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) delete_pose() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) delete_property() (pyrosetta.rosetta.core.chemical.ResidueType method) delete_record() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) delete_region() (in module pyrosetta.rosetta.protocols.grafting) delete_res() (pyrosetta.rosetta.core.pose.PDBInfo method) delete_residue() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) delete_residue_range_slow() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) delete_residue_slow() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) delete_segment() (pyrosetta.rosetta.core.kinematics.FoldTree method) delete_segments() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) delete_self_edges() (pyrosetta.rosetta.core.kinematics.FoldTree method) delete_seqpos() (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.FoldTree method) delete_source_residue() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) delete_submotif_info() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) delete_target_residue() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) delete_terminal_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) delete_this_struct_id() (in module pyrosetta.rosetta.protocols.features.strand_assembly) delete_this_sw_can_by_sh_id_from_sw_by_comp() (in module pyrosetta.rosetta.protocols.features.strand_assembly) delete_unordered_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) delete_upper_padding() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) delete_virtual_residues() (in module pyrosetta.rosetta.protocols.relax) DeleteActCoordAtom (class in pyrosetta.rosetta.core.chemical) DeleteAllRotamerSetOperation (class in pyrosetta.rosetta.core.pack.rotamer_set) DeleteAtom (class in pyrosetta.rosetta.core.chemical) DeleteChainsMover (class in pyrosetta.rosetta.protocols.simple_moves) DeleteChildProton (class in pyrosetta.rosetta.core.chemical) DeleteMetalbindingAtom (class in pyrosetta.rosetta.core.chemical) DeleteMover (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) DeleteProperty (class in pyrosetta.rosetta.core.chemical) DeleteRegionMover (class in pyrosetta.rosetta.protocols.grafting.simple_movers) deletes_atom() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.RenameAtom method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.Set_AA method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) deletes_atoms() (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) deletes_properties() (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) deletes_property() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.RenameAtom method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.Set_AA method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) deletes_variant() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.RenameAtom method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.Set_AA method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) deletes_variants() (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) DeleteTerminalChi (class in pyrosetta.rosetta.core.chemical) DeleteVariantType (class in pyrosetta.rosetta.core.chemical) delta() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) delta_cutoff() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) delta_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) delta_omega0() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) delta_omega1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) delta_omega1_all() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) delta_omega1_vect() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) delta_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) delta_t() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) delta_z1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) delta_z1_vect() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) deltaG_bind() (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) denom() (in module pyrosetta.rosetta.protocols.cryst) DeNovoArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) DeNovoArchitectFactory (class in pyrosetta.rosetta.protocols.denovo_design.architects) DeNovoMotifArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) DenseEnergyContainer (class in pyrosetta.rosetta.core.scoring) DenseNeighborConstIterator (class in pyrosetta.rosetta.core.scoring) DenseNeighborIterator (class in pyrosetta.rosetta.core.scoring) DensitySymmInfo (class in pyrosetta.rosetta.protocols.electron_density) DenyPdbIdFilter (class in pyrosetta.rosetta.protocols.frag_picker) dependencies() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) dependencies_exist() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) dependent_begin() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) dependent_end() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) dependent_on() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) depends_on_a_true_index() (pyrosetta.rosetta.core.chemical.AtomICoor method) depends_on_polymer_lower() (pyrosetta.rosetta.core.chemical.AtomICoor method) depends_on_polymer_upper() (pyrosetta.rosetta.core.chemical.AtomICoor method) depends_on_residue_connection() (pyrosetta.rosetta.core.chemical.AtomICoor method) deposition_date() (pyrosetta.rosetta.core.io.HeaderInformation method) deprecated_eval_atom_derivative() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) depth() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) deriv_check() (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) deriv_check_result() (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.CartesianMinimizer method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) deriv_score() (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) derivative_atom() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) derivatives() (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) derive_from_src_lib() (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) derive_peptide() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) derive_sc_sc_restraints() (in module pyrosetta.rosetta.protocols.relax) derived_dofs() (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) DerivedSequenceMapping (class in pyrosetta.rosetta.core.sequence) DerivVectorPair (class in pyrosetta.rosetta.core.scoring) describe_fragments() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) describe_score() (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) description() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) deserialize() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) deserialize_db_listener_data() (in module pyrosetta.rosetta.protocols.features) deserialize_xyz_coords() (in module pyrosetta.rosetta.protocols.features) design() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method)

design_all_aas() (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) design_antigen() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) design_any() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) design_chain1() (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) design_chain2() (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) design_framework() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) design_loop() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) design_neighbors() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) design_only_target_residues() (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) design_proline() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) design_protocol_to_enum() (in module pyrosetta.rosetta.protocols.antibody.design) design_protocol_to_string() (in module pyrosetta.rosetta.protocols.antibody.design) design_residue() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) designable() (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) DesignContrast (class in pyrosetta.rosetta.core.io.sequence_comparation) designing_residues() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) DesignMeanField (class in pyrosetta.rosetta.protocols.mean_field) DesignMinimizeHbonds (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) DesignRepackMover (class in pyrosetta.rosetta.protocols.calc_taskop_movers) DesignRestrictions (class in pyrosetta.rosetta.core.pack.task.operation) DesignTask (class in pyrosetta.rosetta.protocols.flxbb) DesignTask_Layer (class in pyrosetta.rosetta.protocols.flxbb) DesignTask_Normal (class in pyrosetta.rosetta.protocols.flxbb) DesignVsNativeComparison (class in pyrosetta.rosetta.protocols.enzdes) desired_ala_fraction() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) desired_charge() (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup method) desired_loops() (pyrosetta.rosetta.protocols.LoopRebuild method) desired_min_hydrophobic_fraction() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) desired_remodelres_in_vicinity() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) desired_result() (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle method) (pyrosetta.rosetta.core.chemical.Selector_AA method) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG method) (pyrosetta.rosetta.core.chemical.Selector_HAS_ATOMS method) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_NAME1 method) (pyrosetta.rosetta.core.chemical.Selector_NAME3 method) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY method) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION method) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE method) destination_size() (pyrosetta.rosetta.utility.subset_mapping method) destructed() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) DestructionEvent (class in pyrosetta.rosetta.core.pose.signals) desymmeterize() (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler method) desymmeterize_upstream_restype_for_constraint() (pyrosetta.rosetta.protocols.match.Matcher method) det3() (in module pyrosetta.rosetta.numeric.model_quality) detach() (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) detach_after_modify() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) detach_from() (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) detach_from_conformation() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) detach_impl() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) detach_observer() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) detached_clone() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) detached_copy() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) detect() (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector method) detect_axes() (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) detect_base_contacts() (in module pyrosetta.rosetta.core.pose.rna) detect_bonds() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) detect_disulfides() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) detect_heavy_chain() (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector method) detect_ld_chirality_from_polymer_residue() (in module pyrosetta.rosetta.core.chemical) detect_light_chain() (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector method) detect_phosphate_contacts() (in module pyrosetta.rosetta.core.pose.rna) detect_pseudobonds() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) detect_sugar_contacts() (in module pyrosetta.rosetta.core.pose.rna) DetectProteinLigandInterface (class in pyrosetta.rosetta.protocols.enzdes) determine_atom_inds_for_restype() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) determine_atom_level_edge_info() (in module pyrosetta.rosetta.core.pack.hbonds) determine_atom_level_edge_info_for_all_edges() (in module pyrosetta.rosetta.core.pack.hbonds) determine_atom_level_node_info() (in module pyrosetta.rosetta.core.pack.hbonds) determine_atom_level_node_info_for_all_nodes() (in module pyrosetta.rosetta.core.pack.hbonds) determine_core_heading_surface_heading_by_distance() (in module pyrosetta.rosetta.protocols.features.strand_assembly) determine_cyclization_viability() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) determine_file_type() (in module pyrosetta.rosetta.core.import_pose) determine_heading_direction_by_vector() (in module pyrosetta.rosetta.protocols.features.strand_assembly) determine_job_tag() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter method) determine_largest_nbr_atom_distance() (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) determine_lo_and_hi_residues() (in module pyrosetta.rosetta.core.scoring.methods) determine_loop() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) determine_max_accepted_hbond_count() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) determine_preliminary_job_list_from_xml_file() (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) determine_random_number_seed() (in module pyrosetta.rosetta.core.init) determine_redundant_upstream_matchres() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) determine_score_variations() (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) determine_whether_point_is_buried() (in module pyrosetta.rosetta.core.select.util) dEtot_dEhb() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) deviation() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) dexponential() (in module pyrosetta.rosetta.core.scoring.constraints) dfour1_plan() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) dfs() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) dfunc() (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.Multifunc method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GriddedAtomTreeMultifunc method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc method) dfunc_component() (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) dG_dCi() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) dgaussian() (in module pyrosetta.rosetta.core.scoring.constraints) DGBindOptEData (class in pyrosetta.rosetta.protocols.optimize_weights) DHR_Type (class in pyrosetta.rosetta.protocols.docking) Di() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) DiagnosticData (class in pyrosetta.rosetta.basic.datacache) difference_from() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) different_resgroup() (in module pyrosetta.rosetta.core.pack.rotamer_set) different_restype() (in module pyrosetta.rosetta.core.pack.rotamer_set) differentiate() (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.Expression method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression method) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) Digraph (class in pyrosetta.rosetta.utility.graph) digraph_is_a_DAG() (in module pyrosetta.rosetta.utility.graph) dihedral() (in module pyrosetta.rosetta.numeric) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) dihedral_between_bonded_children() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) dihedral_degrees() (in module pyrosetta.rosetta.numeric) dihedral_degrees_double() (in module pyrosetta.rosetta.numeric) dihedral_diff() (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) dihedral_distance() (in module pyrosetta.rosetta.protocols.idealize) dihedral_double() (in module pyrosetta.rosetta.numeric) dihedral_radians() (in module pyrosetta.rosetta.numeric) dihedral_radians_double() (in module pyrosetta.rosetta.numeric) dihedral_rmsd() (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector method) DihedralConstraint (class in pyrosetta.rosetta.core.scoring.constraints) DihedralConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) DihedralConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) DihedralConstraintsScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) DihedralDistanceMetric (class in pyrosetta.rosetta.protocols.analysis.simple_metrics) DihedralPairConstraint (class in pyrosetta.rosetta.core.scoring.constraints) DihedralPairConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) dihedrals_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) dijkstras() (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) dim() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) dim_labels() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) Dimension (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpression (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionCon (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionCube (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionDiv (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionMax (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionMin (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionMul (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionPow (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionRef (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionSquare (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionSub (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionSum (class in pyrosetta.rosetta.ObjexxFCL) dimOther() (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) dimprod() (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) dimReal() (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) dims() (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) dims_v() (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) dimsizes() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) DipolarCoupling (class in pyrosetta.rosetta.core.scoring) dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) dir() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) DirectedEdgeList (class in pyrosetta.rosetta.utility.graph) DirectedEdgeListConstIterator (class in pyrosetta.rosetta.utility.graph) DirectedEdgeListElement (class in pyrosetta.rosetta.utility.graph) DirectedEdgeListIterator (class in pyrosetta.rosetta.utility.graph) Direction (class in pyrosetta.rosetta.protocols.rigid) direction() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) directory() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) DirectReadoutEnergy (class in pyrosetta.rosetta.core.scoring.methods) DirectReadoutPotential (class in pyrosetta.rosetta.core.scoring.dna) dis() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) dis_U1D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) disable() (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints method) disable_auto_update() (pyrosetta.rosetta.core.scoring.NeighborList method) disable_autotemp() (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) disable_build_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) disable_centroid_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) disable_cis_pro_sampling() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) disable_conserved_framework_positions() (in module pyrosetta.rosetta.protocols.antibody.design) disable_constraint_scoreterms() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) disable_design_antigen() (in module pyrosetta.rosetta.protocols.antibody.design) disable_design_cdr() (in module pyrosetta.rosetta.protocols.antibody.design) disable_design_cdrs() (in module pyrosetta.rosetta.protocols.antibody.design) disable_design_for_non_designing_cdrs() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) disable_design_framework() (in module pyrosetta.rosetta.protocols.antibody.design) disable_design_region() (in module pyrosetta.rosetta.protocols.antibody.design) disable_disallowed_aa() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) disable_fullatom_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) disable_h3_stem_positions() (in module pyrosetta.rosetta.protocols.antibody.design) disable_ignorefinished() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) disable_inprogress() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) disable_output() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) disable_proline_design() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) disable_sampling_of_loop_takeoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) disable_total_energy_cutoff() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) DisableAntibodyRegionOperation (class in pyrosetta.rosetta.protocols.antibody.task_operations) DisableCDRsOperation (class in pyrosetta.rosetta.protocols.antibody.task_operations) disabled_except_during_packing() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) disallow_aas() (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) disallow_movement_of_input_res() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) disallow_noncanonical_aas() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) disallow_pack_polar_hydrogens() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) disallow_quench() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) disallow_realign() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) disallow_resid() (pyrosetta.rosetta.core.pack.task.operation.OptH method) DisallowIfNonnative (class in pyrosetta.rosetta.core.pack.task.operation) discard_conformation_domain_map() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) disconnected_segments() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) discontinued_lower() (in module pyrosetta.rosetta.protocols.hybridization) discontinued_upper() (in module pyrosetta.rosetta.protocols.hybridization) DiscreteRandomizer (class in pyrosetta.rosetta.protocols.genetic_algorithm) DisembodiedAssembly (class in pyrosetta.rosetta.protocols.legacy_sewing) DisplayPoseLabelsMover (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) dist() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) dist_cutoff() (pyrosetta.rosetta.protocols.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborsByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) dist_exponent() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions method) dist_midpoint() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions method) dist_square() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) distance() (in module pyrosetta.rosetta.core.kinematics) (in module pyrosetta.rosetta.core.kinematics.tree) (in module pyrosetta.rosetta.protocols.mpi_refinement) (pyrosetta.rosetta.core.chemical.Bond method) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) distance_cutoff() (pyrosetta.rosetta.numeric.kdtree.KDPointList method) distance_diff() (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) distance_fast() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) distance_from_line2D() (in module pyrosetta.rosetta.core.membrane) distance_internal() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) distance_pair() (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) distance_slow() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) distance_squared() (in module pyrosetta.rosetta.core.kinematics.tree) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) distance_squared_cb() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) distance_squared_cen() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) DistanceChainbreakEnergy (class in pyrosetta.rosetta.core.scoring.methods) DistanceConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) DistancePairConstraint (class in pyrosetta.rosetta.core.scoring.constraints) DistanceResidueNetwork (class in pyrosetta.rosetta.protocols.toolbox) DistanceScoreMover (class in pyrosetta.rosetta.protocols.noesy_assign) distbin_map() (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) distinguish_backbone_and_sidechain_for_node() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) distinguish_pucker() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) Distribution (class in pyrosetta.rosetta.protocols.ligand_docking) DistributionMap (class in pyrosetta.rosetta.protocols.ligand_docking) disulf_atom_index() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) disulfide_bonds() (in module pyrosetta.rosetta.core.conformation) disulfide_pairs() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) DisulfideAtomIndices (class in pyrosetta.rosetta.core.scoring.disulfides) DisulfideCyclizationViability (class in pyrosetta.rosetta.protocols.simple_moves) DisulfideDerivativeAtom (class in pyrosetta.rosetta.core.scoring.disulfides) DisulfideDistance (class in pyrosetta.rosetta.protocols.frag_picker.scores) DisulfideFile (class in pyrosetta.rosetta.core.io.raw_data) DisulfideFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) DisulfideIdentity (class in pyrosetta.rosetta.protocols.frag_picker.scores) DisulfideInsertionMover (class in pyrosetta.rosetta.protocols.simple_moves) DisulfideMatchingEnergyComponents (class in pyrosetta.rosetta.core.scoring.disulfides) DisulfideMatchingNeighborConstIterator (class in pyrosetta.rosetta.core.scoring.disulfides) DisulfideMatchingNeighborIterator (class in pyrosetta.rosetta.core.scoring.disulfides) DisulfideMatchingPotential (class in pyrosetta.rosetta.core.scoring.disulfides) disulfides() (pyrosetta.rosetta.core.io.raw_data.DisulfideFile method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) DisulfJumpClaimer (class in pyrosetta.rosetta.protocols.topology_broker) diversify_all_confs() (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) DiversifyCrmsdByClustering (class in pyrosetta.rosetta.protocols.frag_picker) DiversifyCrmsdSelector (class in pyrosetta.rosetta.protocols.frag_picker) DiversifyDihedralsSelector (class in pyrosetta.rosetta.protocols.frag_picker) DiversifyStoredRBConfs (class in pyrosetta.rosetta.protocols.enzdes) divide_and_conquer() (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) DivideAndConqueror (class in pyrosetta.rosetta.protocols.denovo_design.components) divides_backbone_and_sidechain_energetics() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) dk() (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) dljatr() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) dljrep() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) dna_base_partner() (in module pyrosetta.rosetta.protocols.dna) dna_comp_name_str() (in module pyrosetta.rosetta.protocols.dna) DNA_EnvPairEnergy (class in pyrosetta.rosetta.core.scoring.methods) dna_full_name3() (in module pyrosetta.rosetta.protocols.dna) DnaDesignDef (class in pyrosetta.rosetta.protocols.dna) DnaInterfaceMultiStateDesign (class in pyrosetta.rosetta.protocols.dna) dncase() (in module pyrosetta.rosetta.ObjexxFCL) dnmtr() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) do_apply() (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) do_caching() (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) do_caching_simple() (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) do_correct_NH() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) do_distributed_rerun() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) do_final_fastrelax() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) do_final_repack() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) do_I_skip() (in module pyrosetta.rosetta.protocols.scoring.methods.pcs2) do_not_autoassign_SS() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) do_not_sample_multiple_virtual_sugar() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) do_one_line() (in module pyrosetta.rosetta.protocols.frag_picker.scores) do_packing() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) do_prepack() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) do_rerun() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) do_score() (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) do_scoring() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) do_set_xyz() (in module pyrosetta.rosetta.protocols.stepwise.sampler.protein) do_xy_scan() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) dock_domain_map() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) dock_high_res() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) dock_low_res() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) docking_highres_filter() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) docking_highres_mover() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) docking_lowres_filter() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) docking_lowres_mover() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) DockingEnsemble (class in pyrosetta.rosetta.protocols.docking) DockingHighResFactory (class in pyrosetta.rosetta.protocols.docking) DockingHighResFilter (class in pyrosetta.rosetta.protocols.docking) DockingHighResLegacy (class in pyrosetta.rosetta.protocols.docking) DockingInitialPerturbation (class in pyrosetta.rosetta.protocols.docking) DockingLowResFilter (class in pyrosetta.rosetta.protocols.docking) DockingProtocol (class in pyrosetta.rosetta.protocols.docking) DockingSlideIntoContact (class in pyrosetta.rosetta.protocols.docking) DockIntoDensityMover (class in pyrosetta.rosetta.protocols.electron_density) dockPoseIntoMap() (in module pyrosetta.rosetta.protocols.electron_density) DockSetupMover (class in pyrosetta.rosetta.protocols.docking) DockWithHotspotMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) dof() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) DOF_bin_size() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body) DOF_bin_value() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body) DOF_Constraint (class in pyrosetta.rosetta.core.scoring.constraints) dof_deriv_1benmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationNode method) dof_deriv_1benmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationNode method) dof_deriv_2benmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationNode method) dof_deriv_2benmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationNode method) DoF_helix_index() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) DOF_ID (class in pyrosetta.rosetta.core.id) dof_id() (pyrosetta.rosetta.core.id.DOF_ID_Range method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint method) dof_id_begin() (pyrosetta.rosetta.core.kinematics.MoveMap method) dof_id_end() (pyrosetta.rosetta.core.kinematics.MoveMap method) dof_id_from_atom_ids() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) dof_id_from_torsion_id() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) DOF_ID_Range (class in pyrosetta.rosetta.core.id) DoF_name() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) dof_node_from_id() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) dof_nodes() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) DoF_sample_value() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) dof_type (class in pyrosetta.rosetta.core.conformation.symmetry) DOF_Type (class in pyrosetta.rosetta.core.id) DoF_type() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) dof_type_begin() (pyrosetta.rosetta.core.kinematics.MoveMap method) dof_type_end() (pyrosetta.rosetta.core.kinematics.MoveMap method) DOF_type_is_rb() (in module pyrosetta.rosetta.core.id) dofs() (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) dofs_to_vars() (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) DoFType (class in pyrosetta.rosetta.protocols.helical_bundle) dofType (class in pyrosetta.rosetta.protocols.jumping) domain_map() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.NeighborList method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) DomainAssembly (class in pyrosetta.rosetta.protocols.abinitio) don_bbg_in_bb_bb_hbond() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) donor_acceptor_group() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) donor_acceptor_groups() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) donor_acceptor_groups_equivalent_res_symmetry_copy_hbonds_accepted() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) donor_acceptor_groups_equivalent_res_symmetry_copy_hbonds_donated() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) donor_acceptor_groups_intrares_hbonds_accepted() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) donor_acceptor_groups_intrares_hbonds_donated() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) donor_group() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond method) donor_selector() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) donor_symmetry_copy_index() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond method) dont_be_lenient() (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) dont_check_overlap() (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) dont_check_rama() (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) dot() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.numeric.kinematic_closure) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) dot_abs() (pyrosetta.rosetta.core.scoring.EnergyEdge method) dot_coord() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) dot_exposed() (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) DotSphere (class in pyrosetta.rosetta.core.pack.interaction_graph) double_lazy_ig() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) double_lazy_ig_memlimit() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) double_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) DoubleLazyInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) down_cast() (in module pyrosetta.rosetta.utility) downstream() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) downstream_atom() (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.kinematics.FoldTree method) downstream_builder() (pyrosetta.rosetta.protocols.match.Matcher method) downstream_builders() (pyrosetta.rosetta.protocols.match.Matcher method) downstream_centroid_by_jump() (in module pyrosetta.rosetta.protocols.geometry) downstream_combine() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) downstream_jump_residue() (pyrosetta.rosetta.core.kinematics.FoldTree method) downstream_jump_stub() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) downstream_pose() (pyrosetta.rosetta.protocols.match.Matcher method) downstream_residues_from_jump() (in module pyrosetta.rosetta.protocols.hybridization) DownstreamAlgorithm (class in pyrosetta.rosetta.protocols.match.downstream) DownstreamRMSEvaluator (class in pyrosetta.rosetta.protocols.match.output) drift() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) drop_all_edges() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) drop_all_edges_for_node() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) drop_constraints() (in module pyrosetta.rosetta.core.scoring.constraints) drop_edge() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) drop_rotamer() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) drop_rotamers() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) drop_rotamers_by_index() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) drop_strand_pairs() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) drop_unsatisfied_voxels() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) dround() (in module pyrosetta.rosetta.core.scoring.rna.chemical_shift) dry_run() (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) ds_hitset_end_its() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) ds_hitset_its() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) dSA_dDi() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) dscore() (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore method) dslfc_ang() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) dslfc_bb_dih() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) dslfc_cb_dih() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) dslfc_cb_dst() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) dslfc_cen_dst() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) dslfc_rot() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents method) dslfc_RT() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents method) dslfc_trans() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents method) dsolv() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) dsolv1() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) dsolv2() (pyrosetta.rosetta.core.scoring.etable.MembEtable method) dsolv_dBR() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) Dssp (class in pyrosetta.rosetta.core.scoring.dssp) dssp() (in module pyrosetta.rosetta.protocols.simple_filters) (pyrosetta.rosetta.core.scoring.dssp.Dssp method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) dssp_featurizer() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) dssp_phi() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) dssp_psi() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) dssp_reduced() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) dssp_reduced_IG_as_L() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) dssp_reduced_IG_as_L_if_adjcent_H() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) dssp_state() (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) DsspDesignOperation (class in pyrosetta.rosetta.protocols.task_operations) DualMonteCarlo (class in pyrosetta.rosetta.protocols.moves) dummy_modify() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) dump() (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.Multifunc method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc method) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GriddedAtomTreeMultifunc method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) dump_as_pdb() (in module pyrosetta.rosetta.protocols.toolbox) dump_atom_pair_energy_table() (in module pyrosetta) dump_atom_tree_diff() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) dump_cif() (in module pyrosetta.rosetta.core.io.mmcif) (pyrosetta.rosetta.core.pose.Pose method) dump_comment_pdb() (in module pyrosetta.rosetta.core.pose) dump_cst_file() (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) dump_eggshell() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) dump_file() (pyrosetta.rosetta.core.pose.Pose method) dump_frames_as_pdb() (in module pyrosetta.rosetta.core.fragment) dump_gws() (in module pyrosetta.rosetta.core.io.carbohydrates) dump_gws_chain() (in module pyrosetta.rosetta.core.io.carbohydrates) dump_invrots_tree_as_multimodel_pdbs() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) dump_loophash_linkers() (in module pyrosetta.rosetta.protocols.sic_dock) dump_multimodel_pdb() (in module pyrosetta.rosetta.core.io.pdb) dump_packertask() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) dump_pdb() (in module pyrosetta.rosetta.core.io.pdb) (pyrosetta.rosetta.core.pose.Pose method) dump_pdb_residue() (in module pyrosetta.rosetta.core.io.pdb) dump_points_pdb() (in module pyrosetta.rosetta.protocols.sic_dock) dump_pose() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) dump_pose_and_map() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) dump_pose_kinemage() (in module pyrosetta.rosetta.protocols.viewer) dump_reference_pose() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) dump_residue_pair_energies() (in module pyrosetta) dump_score_line() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) dump_scored_pdb() (pyrosetta.rosetta.core.pose.Pose method) dump_silent() (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) dump_vall_fasta() (in module pyrosetta.rosetta.protocols.frags) dump_vd_info() (pyrosetta.rosetta.core.chemical.ResidueType method) dump_weights() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) dumpExemplarToFile() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) dumpGridToFile() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) DumpPdb (class in pyrosetta.rosetta.protocols.simple_moves) DumpSingleResidueRotamers (class in pyrosetta.rosetta.protocols.simple_moves) dumpTargetPocketsToFile() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) dumpTargetPocketsToPDB() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) DumpTrajectoryEnergy (class in pyrosetta.rosetta.core.scoring.util_methods) dunbrack_print() (in module pyrosetta.rosetta.protocols.make_rot_lib) DunbrackAAParameterSet (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackConstraintCreator (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackSCSampler (class in pyrosetta.rosetta.protocols.match.upstream) dweight() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) dx_ddelta_omega1() (in module pyrosetta.rosetta.numeric.crick_equations) dx_ddelta_z1() (in module pyrosetta.rosetta.numeric.crick_equations) dx_ddz1() (in module pyrosetta.rosetta.numeric.crick_equations) dx_domega1() (in module pyrosetta.rosetta.numeric.crick_equations) dx_dr1() (in module pyrosetta.rosetta.numeric.crick_equations) dy_ddelta_omega1() (in module pyrosetta.rosetta.numeric.crick_equations) dy_ddelta_z1() (in module pyrosetta.rosetta.numeric.crick_equations) dy_ddz1() (in module pyrosetta.rosetta.numeric.crick_equations) dy_domega1() (in module pyrosetta.rosetta.numeric.crick_equations) dy_dr1() (in module pyrosetta.rosetta.numeric.crick_equations) dynamic_memory_usage() (pyrosetta.rosetta.utility.recent_history_queue method) DynamicIndexRange (class in pyrosetta.rosetta.ObjexxFCL) dz_ddelta_omega1() (in module pyrosetta.rosetta.numeric.crick_equations) dz_ddelta_z1() (in module pyrosetta.rosetta.numeric.crick_equations) dz_ddz1() (in module pyrosetta.rosetta.numeric.crick_equations) dz_domega1() (in module pyrosetta.rosetta.numeric.crick_equations) dz_dr1() (in module pyrosetta.rosetta.numeric.crick_equations)

E

E() (in module pyrosetta.rosetta.ObjexxFCL.format) e1() (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) e2() (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) E_elec() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) E_solv() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) E_solv_pair() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) E_solv_self() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) EBC_ClusterType (class in pyrosetta.rosetta.protocols.energy_based_clustering) Edge (class in pyrosetta.rosetta.core.kinematics) edge() (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) edge_label() (pyrosetta.rosetta.core.kinematics.FoldTree method) edge_list_begin() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) edge_list_end() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) edge_list_iterator_at_end() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) edge_satisfies_heavy_unsat_for_node() (in module pyrosetta.rosetta.protocols.hbnet) EdgeList (class in pyrosetta.rosetta.utility.graph) EdgeListConstIterator (class in pyrosetta.rosetta.utility.graph) EdgeListElement (class in pyrosetta.rosetta.utility.graph) EdgeListIterator (class in pyrosetta.rosetta.utility.graph) effective_lower_terminus_based_on_working_res() (in module pyrosetta.rosetta.core.pose) effective_sequence_separation() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) effective_upper_terminus_based_on_working_res() (in module pyrosetta.rosetta.core.pose) Efield_fixed() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) Efield_induced() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) Efield_rf_fixed() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) Efield_rf_induced() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) eggshell_coord_list() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) EggshellGrid (class in pyrosetta.rosetta.protocols.pockets) Ei() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) eigenvalue_jacobi() (in module pyrosetta.rosetta.numeric) eigenvector_jacobi() (in module pyrosetta.rosetta.numeric) EItem (class in pyrosetta.rosetta.core.optimization) elapsed_time() (pyrosetta.rosetta.protocols.jd2.Job method) elec_die() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) elec_group_file() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) elec_max_dis() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) elec_min_dis() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) elec_no_dis_dep_die() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) elec_sigmoidal_die() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) elec_sigmoidal_die_params() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) elecF2() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) ElectronConfiguration (class in pyrosetta.rosetta.core.chemical) ElectronConfiguration.AngularMomentumQuantumNumber (class in pyrosetta.rosetta.core.chemical) ElectronConfiguration.PrincipalQuantumNumber (class in pyrosetta.rosetta.core.chemical) elem_length() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) Element (class in pyrosetta.rosetta.core.chemical) element() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.ElementSet method) Element.Properties (class in pyrosetta.rosetta.core.chemical) element2name() (in module pyrosetta.rosetta.core.chemical.element) element_from_string() (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory method) element_index() (pyrosetta.rosetta.core.chemical.ElementSet method) element_list() (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) element_name() (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement method) element_set() (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) element_set_ptr() (pyrosetta.rosetta.core.chemical.ResidueType method) element_summary_as_simple_subelement() (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) element_type() (pyrosetta.rosetta.core.chemical.Atom method) element_type_def() (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) Elements (class in pyrosetta.rosetta.core.chemical.element) elements_from_name() (in module pyrosetta.rosetta.core.chemical.element) ElementSet (class in pyrosetta.rosetta.core.chemical) EllipsoidalRandomizationMover (class in pyrosetta.rosetta.protocols.docking) EMapVector (class in pyrosetta.rosetta.core.scoring) EmbeddingDef (class in pyrosetta.rosetta.protocols.membrane.geometry) emergency_rotamer() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) emit_intermediate() (in module pyrosetta.rosetta.protocols.nonlocal) (in module pyrosetta.rosetta.protocols.star) Emitter (class in pyrosetta.rosetta.basic) EMPTY (class in pyrosetta.rosetta.core.pack.task) empty() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.signals.Link method) empty_clone() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) empty_pose() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) empty_record() (pyrosetta.rosetta.core.pose.PDBInfo method) empty_sfxn() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) enable() (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints method) enable_autotemp() (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) enable_benchmark_mode() (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) enable_build_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) enable_centroid_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) enable_constraint_scoreterms() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) enable_custom_variant_types() (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueType method) enable_end_bias_check() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) enable_fullatom_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) enable_graft_h1() (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) enable_graft_h2() (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) enable_graft_h3() (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) enable_graft_l1() (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) enable_graft_l2() (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) enable_graft_l3() (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) enable_ignorefinished() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) enable_inprogress() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) enable_MPI_reroute() (pyrosetta.rosetta.utility.io.ozstream method) enable_output() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) enable_sampling_of_loop_takeoff() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close) enabled() (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) EnableMultiCoolAnnealer (class in pyrosetta.rosetta.core.pack.task.operation) enclosing_angles() (in module pyrosetta.rosetta.core.membrane) encode6bit() (in module pyrosetta.rosetta.utility) encode_24_to_32() (in module pyrosetta.rosetta.utility) end() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.jumping.Interval method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) end1() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) end_atomid() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) end_atoms1() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) end_atoms2() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) end_bias() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) end_bias_check() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) end_bias_check_enabled() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) end_bias_probabilities() (in module pyrosetta.rosetta.protocols.medal) end_const() (pyrosetta.rosetta.core.io.raw_data.RawFileData method) end_critical_section() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) end_list() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) end_map() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) end_of_queue() (pyrosetta.rosetta.utility.recent_history_queue method) end_output_writing() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) end_receptor_partner_pair() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) end_res() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) end_structure() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) end_time() (pyrosetta.rosetta.protocols.jd2.Job method) end_timing() (pyrosetta.rosetta.protocols.jd2.Job method) ending_node() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) endswith() (in module pyrosetta.rosetta.utility) EndToEndPivots (class in pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers) Energies (class in pyrosetta.rosetta.core.scoring) energies() (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.pose.Pose method) energies_from_pose() (pyrosetta.rosetta.core.io.silent.SilentStruct method) energies_into_pose() (pyrosetta.rosetta.core.io.silent.SilentStruct method) energies_matrix() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) energies_not_yet_computed() (pyrosetta.rosetta.core.scoring.EnergyEdge method) energies_updated() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) energy() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) energy_computed() (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) energy_cutoff() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) energy_from_pose() (in module pyrosetta.rosetta.core.pose) energy_graph() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) energy_matrices() (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) energy_matrix() (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) energy_method_options() (pyrosetta.rosetta.core.scoring.ScoreFunction method) energy_names() (pyrosetta.rosetta.core.io.silent.SilentStruct method) energy_terms() (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) EnergyBasedClusteringOptions (class in pyrosetta.rosetta.protocols.energy_based_clustering) EnergyBasedClusteringProtocol (class in pyrosetta.rosetta.protocols.energy_based_clustering) EnergyCutRotamerTrialsMinMover (class in pyrosetta.rosetta.protocols.minimization_packing) EnergyEdge (class in pyrosetta.rosetta.core.scoring) EnergyEval (class in pyrosetta.rosetta.core.fragment.picking_old.vall.eval) EnergyEvent (class in pyrosetta.rosetta.core.pose.signals) EnergyGraph (class in pyrosetta.rosetta.core.scoring) EnergyLandscapeEvaluator (class in pyrosetta.rosetta.protocols.toolbox) EnergyMethod (class in pyrosetta) (class in pyrosetta.rosetta.core.scoring.methods) EnergyMethodCreator (class in pyrosetta.rosetta.core.scoring.methods) EnergyMethodOptions (class in pyrosetta.rosetta.core.scoring.methods) EnergyMethods (class in pyrosetta.rosetta.core.scoring.methods) EnergyMethodType (class in pyrosetta.rosetta.core.scoring.methods) EnergyNode (class in pyrosetta.rosetta.core.scoring) EnergyReporter (class in pyrosetta.rosetta.protocols.pose_reporters) enforce_all_waters() (in module pyrosetta.rosetta.protocols.hydrate) enforce_minimum_length() (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) enlarge_h_lj_wdepth() (in module pyrosetta.rosetta.core.chemical) enough_connections() (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) enqueue() (pyrosetta.rosetta.protocols.moves.CyclicMover method) EnsembleJobInputter (class in pyrosetta.rosetta.protocols.jd2) ensure_directory_for_out_silent_file_exists() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) ensure_phosphate_nomenclature_matches_mini() (in module pyrosetta.rosetta.protocols.rna.denovo) ensure_site() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) ensure_size() (pyrosetta.rosetta.core.optimization.Particle method) ensure_valid_full_seq_num() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) Entity (class in pyrosetta.rosetta.protocols.genetic_algorithm) entity_elements_from_1letterstring() (in module pyrosetta.rosetta.protocols.multistate_design) entity_length() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) entity_template() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) EntityElement (class in pyrosetta.rosetta.protocols.genetic_algorithm) EntityElementCreator (class in pyrosetta.rosetta.protocols.genetic_algorithm) EntityElementFactory (class in pyrosetta.rosetta.protocols.genetic_algorithm) EntityRandomizer (class in pyrosetta.rosetta.protocols.genetic_algorithm) Enum (class in pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType) (class in pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType) (class in pyrosetta.rosetta.protocols.forge.build.BuildInstructionState) (class in pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme) (class in pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage) (class in pyrosetta.rosetta.protocols.jd2.JobInputterInputSource) enumerate() (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) enumerate_permutations() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) enumeration_shell() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) envsmooth_zero_negatives() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) enz_io() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) EnzConstraintParameters (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) enzcst_io() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) EnzCstTemplateRes (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) EnzCstTemplateResAtoms (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) EnzdesCstCache (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) EnzdesJobOutputter (class in pyrosetta.rosetta.protocols.enzdes) EnzdesLoopsFile (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) EnzdesScorefileFilter (class in pyrosetta.rosetta.protocols.enzdes) EnzymaticMover (class in pyrosetta.rosetta.protocols.enzymatic_movers) EnzymeData (class in pyrosetta.rosetta.core.enzymes) EnzymeManager (class in pyrosetta.rosetta.core.enzymes) eof() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) epsilon() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) epsilon_aform() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) epsilon_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) epsilon_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) epslon() (in module pyrosetta.rosetta.numeric.linear_algebra) equal() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) equal_by_epsilon() (in module pyrosetta.rosetta.numeric) equal_size() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) equali() (in module pyrosetta.rosetta.ObjexxFCL) equals() (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) equals_string() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) EqualsExpression (class in pyrosetta.rosetta.numeric.expression_parser) erase() (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) erase_comment() (pyrosetta.rosetta.core.io.silent.SilentStruct method) erase_hit() (pyrosetta.rosetta.protocols.match.Matcher method) erfcc() (in module pyrosetta.rosetta.numeric.model_quality) errf() (in module pyrosetta.rosetta.numeric.statistics) errfc() (in module pyrosetta.rosetta.numeric.statistics) errfcx() (in module pyrosetta.rosetta.numeric.statistics) errfi() (in module pyrosetta.rosetta.numeric.statistics) Error() (in module pyrosetta.rosetta.basic) error() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method)

error_check_requested_adducts() (in module pyrosetta.rosetta.core.chemical) error_on_out_of_bounds_index() (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) esolvE() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) EST_THRESHOLD_MODE (class in pyrosetta.rosetta.protocols.cluster.calibur) estimate_dfunc() (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) estimate_membrane_center() (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) estimate_sidechain_depth() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) Etable (class in pyrosetta.rosetta.core.scoring.etable) etable_atom_pair_energies() (in module pyrosetta) etable_disbins() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) etable_energy() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) etable_options() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) etable_type() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) EtableEvaluator (class in pyrosetta.rosetta.core.scoring.etable) EtableFunc (class in pyrosetta.rosetta.core.scoring.func) EtableParamsOnePair (class in pyrosetta.rosetta.core.scoring.etable) euler_offsets() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) eval() (pyrosetta.rosetta.protocols.jumping.SameStrand method) eval_atom_derivative() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.GenBornPotential method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) eval_atom_derivative_base_base() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) eval_atom_derivative_rna_backbone_backbone() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) eval_atom_derivative_rna_base_backbone() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) eval_atom_derivative_rna_repulsive() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) eval_atom_derivatives_for_minedge() (in module pyrosetta.rosetta.core.scoring) eval_atom_derivatives_for_minnode() (in module pyrosetta.rosetta.core.scoring) eval_atom_nonpolar_derivative() (pyrosetta.rosetta.core.scoring.FACTSPotential method) eval_atom_polar_derivative() (pyrosetta.rosetta.core.scoring.FACTSPotential method) eval_bbbb_sr2b_energies() (in module pyrosetta.rosetta.core.scoring) eval_bbsc_sr2b_energies() (in module pyrosetta.rosetta.core.scoring) eval_cd_1b() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_cd_2b() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_cd_2b_bb_bb() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_cd_2b_bb_sc() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_cd_2b_sc_sc() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_cd_intrares_energy() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_ci_1b() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_ci_2b() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_ci_2b_bb_bb() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_ci_2b_bb_sc() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_ci_2b_sc_sc() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_ci_intrares_energy() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_cubic_polynomial() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) eval_dE_dR_over_r_v() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) eval_dof_deriv_for_minnode() (in module pyrosetta.rosetta.core.scoring) eval_dof_derivative() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_impl() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) eval_intrares_derivatives() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) eval_intrares_elec_ST_only() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) eval_intrares_energy() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) eval_intrares_energy_ext() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) eval_intraresidue_dof_derivative() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) eval_intrsres_elec_ST_only() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) eval_long_range_twobody_energies() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_lowest_score_pose() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) eval_multibody_atom_derivative() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) eval_non_residue_pair_energy() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) eval_npd_atom_derivative() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_onebody_energies() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_res() (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) eval_res_onebody_energies_for_minnode() (in module pyrosetta.rosetta.core.scoring) eval_res_pair_energy_for_minedge() (in module pyrosetta.rosetta.core.scoring) eval_residue_derivatives() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) eval_residue_dof_derivative() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) eval_residue_pair_derivatives() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) eval_residue_pair_derivatives_sorted() (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) eval_rna_base_pair_energy() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) eval_rotameric_energy_bb_dof_deriv() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) eval_rotameric_energy_deriv() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) eval_scsc_sr2b_energies() (in module pyrosetta.rosetta.core.scoring) eval_twobody_neighbor_energies() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_weighted_atom_derivatives_for_minedge() (in module pyrosetta.rosetta.core.scoring) eval_weighted_dof_deriv_for_minnode() (in module pyrosetta.rosetta.core.scoring) eval_weighted_res_onebody_energies_for_minnode() (in module pyrosetta.rosetta.core.scoring) eval_weighted_res_pair_energy_for_minedge() (in module pyrosetta.rosetta.core.scoring) evalpoly() (in module pyrosetta.rosetta.numeric.kinematic_closure) evaluate() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) evaluate_cbeta() (pyrosetta.rosetta.core.scoring.MembranePotential method) evaluate_constraints() (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) evaluate_contact_score() (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) evaluate_derivative() (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction method) evaluate_env() (pyrosetta.rosetta.core.scoring.MembranePotential method) evaluate_env_and_cbeta_deriv() (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) evaluate_env_and_cbeta_scores() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) evaluate_env_score() (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) evaluate_local() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) evaluate_nonpolar_energy() (pyrosetta.rosetta.core.scoring.FACTSPotential method) evaluate_pair() (pyrosetta.rosetta.core.scoring.MembranePotential method) evaluate_pair_and_cenpack_deriv() (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) evaluate_pair_and_cenpack_score() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) evaluate_pair_and_vdw_score() (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) evaluate_polar_energy() (pyrosetta.rosetta.core.scoring.FACTSPotential method) evaluate_polar_otf_energy() (pyrosetta.rosetta.core.scoring.FACTSPotential method) evaluate_pose() (in module pyrosetta.rosetta.protocols.evaluation) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) evaluate_positive_states() (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) evaluate_residues() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) evaluate_rnp_aa_rna_backbone_score() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) evaluate_rnp_base_pair_score() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) evaluate_rnp_pair_dist_score() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPairDistPotential method) evaluate_rnp_pair_score() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) evaluate_rotamer_background_energies() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) evaluate_rotamer_background_energy_maps() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) evaluate_rotamer_intrares_energies() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) evaluate_rotamer_intrares_energy_maps() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) evaluate_rotamer_pair_energies() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) evaluate_silent_struct() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) EvaluatedArchive (class in pyrosetta.rosetta.protocols.jd2.archive) evaluator() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) EvaluatorCreator (class in pyrosetta.rosetta.protocols.evaluation) EvaluatorFactory (class in pyrosetta.rosetta.protocols.evaluation) evaluators() (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) events() (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) EventType (class in pyrosetta.rosetta.core.scoring.packstat) EX (class in pyrosetta.rosetta.core.pack.task) ex() (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) ex1() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex1_sample_level() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex1aro() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex1aro_exposed() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex1aro_exposed_sample_level() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex1aro_sample_level() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex2() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex2_sample_level() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex2aro() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex2aro_exposed() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex2aro_exposed_sample_level() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex2aro_sample_level() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex3() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex3_sample_level() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex4() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex4_sample_level() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) EX_CUTOFF (class in pyrosetta.rosetta.core.pack.task) examine_pose() (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) exchange_grid_dim() (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) exclude_AA_threshold() (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) exclude_chain_termini() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) exclude_clusters() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_clusters_add() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_clusters_clear() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_DNA_DNA() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) exclude_exposed() (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) exclude_germlines() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_germlines_add() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_germlines_clear() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_intra_res_protein() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) exclude_monomer_fa_elec() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) exclude_pdbs() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_pdbs_add() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_pdbs_clear() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_protein_protein_fa_elec() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) exclude_RNA_protein_fa_elec() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) exclude_RNA_RNA_fa_elec() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) exclude_site() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) exclude_species() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_species_add() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_species_clear() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_variants() (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) EXCN_CalcFailed (class in pyrosetta.rosetta.protocols.simple_filters) EXCN_Fold (class in pyrosetta.rosetta.protocols.denovo_design.components) EXCN_InitFailed (class in pyrosetta.rosetta.protocols.simple_filters) EXCN_Membrane (class in pyrosetta.rosetta.core.conformation.membrane) EXCN_Membrane_Bounds (class in pyrosetta.rosetta.core.conformation.membrane) EXCN_MembraneFoldTree (class in pyrosetta.rosetta.core.conformation.membrane) EXCN_NonMembrane (class in pyrosetta.rosetta.core.conformation.membrane) EXCN_Resource_Definition (class in pyrosetta.rosetta.core.conformation.membrane) EXCN_Stop_BFS (class in pyrosetta.rosetta.utility.graph) EXCN_VirtualRsd (class in pyrosetta.rosetta.core.conformation.membrane) exdna_sample_level() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) exec() (pyrosetta.rosetta.core.scoring.APBSWrapper method) execute() (in module pyrosetta.rosetta.basic) ExecutionResult (class in pyrosetta.rosetta.basic) Exemplar (class in pyrosetta.rosetta.protocols.cluster) exit() (in module pyrosetta.rosetta.utility) exit_callback() (pyrosetta.rosetta.utility.py.PyExitCallback method) exit_if_missing_heavy_atoms() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) exp() (pyrosetta.rosetta.ObjexxFCL.Dimension method) exp_clone() (pyrosetta.rosetta.ObjexxFCL.Dimension method) exp_hash() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) exp_p() (pyrosetta.rosetta.ObjexxFCL.Dimension method) expand_loop_takeoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) expand_proton_chis() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) expected_by_properties_absolute() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) expected_by_properties_fraction() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) experimental_technique_in_progress() (pyrosetta.rosetta.core.io.HeaderInformation method) experimental_technique_to_string() (pyrosetta.rosetta.core.io.HeaderInformation method) experimental_techniques() (pyrosetta.rosetta.core.io.HeaderInformation method) expid() (pyrosetta.rosetta.core.scoring.RDC method) explicit_links_from_sfr_linkage() (in module pyrosetta.rosetta.core.io) explicit_ramp_constraints() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) explicitly_set_movemap() (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) exponential_deriv() (in module pyrosetta.rosetta.core.scoring.constraints) export_packer_results() (in module pyrosetta.rosetta.protocols.rna.denovo) Expression (class in pyrosetta.rosetta.numeric.expression_parser) ExpressionCreator (class in pyrosetta.rosetta.numeric.expression_parser) ext() (pyrosetta.rosetta.utility.file.FileName method) extend() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) extend_CDR() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) extend_sequence_mapping() (in module pyrosetta.rosetta.protocols.loops) extend_to() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) extended_loop() (pyrosetta.rosetta.protocols.LoopRebuild method) ExtendedPoseBuilder (class in pyrosetta.rosetta.protocols.denovo_design.components) extension() (pyrosetta.rosetta.utility.file.FileName method) external_sampler() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) ExternalGeomSampler (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) ExternalTransform (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) extra_broker_files() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) extra_chi() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) extra_coord_list() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) extra_data_1() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) extra_data_2() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) extra_data_3() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) extra_minimize_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) extra_parameter() (pyrosetta.rosetta.core.chemical.AtomType method) extra_parameter_index() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) extra_parameter_indices() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) extra_residues_to_steal() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) extrachi_cutoff() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) extrachi_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ExtraChiCutoff (class in pyrosetta.rosetta.core.pack.task.operation) extract_asymmetric_unit() (in module pyrosetta.rosetta.core.pose.symmetry) extract_asymmetric_unit_pdb_info() (in module pyrosetta.rosetta.core.pose.symmetry) extract_continuous_chunks() (in module pyrosetta.rosetta.protocols.loops) extract_coordinates_from_pose_1x3() (in module pyrosetta.toolbox.extract_coords_pose) extract_coordinates_from_pose_3x1() (in module pyrosetta.toolbox.extract_coords_pose) extract_fragment() (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) extract_int() (in module pyrosetta.rosetta.protocols.denovo_design) extract_rt() (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) extract_sasa_for_atom() (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) extract_secondary_structure_chunks() (in module pyrosetta.rosetta.protocols.loops) extract_sheets_from_pose() (in module pyrosetta.rosetta.protocols.denovo_design.components) extract_sheets_from_strandlist() (in module pyrosetta.rosetta.protocols.denovo_design.components) extract_tag_from_pose() (in module pyrosetta.rosetta.core.pose) ExtractAsymmetricUnitMover (class in pyrosetta.rosetta.protocols.symmetry) ExtractSmallest() (in module pyrosetta.rosetta.protocols.toolbox) ExtraQuadraticRepulsion (class in pyrosetta.rosetta.core.scoring.etable) ExtraRotamers (class in pyrosetta.rosetta.core.pack.task.operation) ExtraRotamersGeneric (class in pyrosetta.rosetta.core.pack.task.operation) ExtraRotSample (class in pyrosetta.rosetta.core.pack.task) ExtraScoreEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters)

F

F() (in module pyrosetta.rosetta.ObjexxFCL.format) f0() (pyrosetta.rosetta.core.scoring.electron_density.KromerMann method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann method) f1() (pyrosetta.rosetta.core.scoring.DerivVectorPair method) f1ij() (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) f2() (pyrosetta.rosetta.core.scoring.DerivVectorPair method) f2ij() (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) f3ij() (pyrosetta.rosetta.core.scoring.CSA method) fa_center() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_depth() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_dun_cutoff() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) fa_hatr() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) Fa_Membed_update() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_penalty() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_proj() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_proj_coord() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_proj_deriv() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_stack_base_all() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) FabConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) factorA() (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) factorB() (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) factorsLTE19() (in module pyrosetta.rosetta.core.scoring.electron_density) (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) factorsLTE5() (in module pyrosetta.rosetta.core.scoring.electron_density) (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) factory_name() (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory method) factory_register() (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory method) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory method) FACTSPoseInfo (class in pyrosetta.rosetta.core.scoring) FACTSPotential (class in pyrosetta.rosetta.core.scoring) FACTSResidueInfo (class in pyrosetta.rosetta.core.scoring) FACTSRotamerSetInfo (class in pyrosetta.rosetta.core.scoring) FACTSRsdTypeInfo (class in pyrosetta.rosetta.core.scoring) FACTSRsdTypeMap (class in pyrosetta.rosetta.core.scoring) fade_energy() (in module pyrosetta.rosetta.core.scoring.hbonds) FadeInterval (class in pyrosetta.rosetta.core.scoring.hbonds) FaDockingSlideIntoContact (class in pyrosetta.rosetta.protocols.docking) fafilter() (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) fail() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) fake_hit() (in module pyrosetta.rosetta.protocols.match) False (class in pyrosetta.rosetta.utility.type_traits.has_insertion_operator_implementation) false_movemap() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) FaMPEnvEnergy (class in pyrosetta.rosetta.core.scoring.membrane) FaMPEnvEnergyCreator (class in pyrosetta.rosetta.core.scoring.membrane) FaMPEnvSmoothEnergy (class in pyrosetta.rosetta.core.scoring.membrane) FaMPEnvSmoothEnergyCreator (class in pyrosetta.rosetta.core.scoring.membrane) FaMPSolvEnergy (class in pyrosetta.rosetta.core.scoring.membrane) FaMPSolvEnergyCreator (class in pyrosetta.rosetta.core.scoring.membrane) FAScatter (class in pyrosetta.rosetta.core.scoring.fiber_diffraction) fasol_cubic_poly_far_xhi() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) fasol_cubic_poly_far_xlo() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) fast() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) fast_ccd_close_loops() (in module pyrosetta.rosetta.protocols.loops.loop_mover.perturb) fast_forward() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) fast_forward_to_next_residue_pair() (in module pyrosetta.rosetta.protocols.stepwise.screener) fast_rmsd() (in module pyrosetta.rosetta.protocols.cluster.calibur) fast_scan() (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) FastGapMover (class in pyrosetta.rosetta.protocols.loophash) FaSymDockingSlideTogether (class in pyrosetta.rosetta.protocols.symmetry) FavorNativeResidue (class in pyrosetta.rosetta.protocols.protein_interface_design) FavorNonNativeResidue (class in pyrosetta.rosetta.protocols.protein_interface_design) fcen10() (pyrosetta.rosetta.core.scoring.CenListInfo method) fcen12() (pyrosetta.rosetta.core.scoring.CenListInfo method) fcen6() (pyrosetta.rosetta.core.scoring.CenListInfo method) features_reporter_dependencies() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) features_reporter_xml_schema_group_name() (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) FeaturesReporterCreator (class in pyrosetta.rosetta.protocols.features) FeaturesReporterFactory (class in pyrosetta.rosetta.protocols.features) featurizer_state() (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) fetch_stored_derivatives() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) fft3() (in module pyrosetta.rosetta.numeric.fourier) fft3_dynamic() (in module pyrosetta.rosetta.numeric.fourier) figure_out_base_pair_partner() (in module pyrosetta.rosetta.protocols.rna.denovo) figure_out_chain_numbers_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) figure_out_chain_numbers_from_full_model_info_const() (in module pyrosetta.rosetta.core.pose.full_model_info) figure_out_conventional_chains_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) figure_out_dock_domain_map() (in module pyrosetta.rosetta.core.import_pose) figure_out_dock_domain_map_from_full_model_info_const() (in module pyrosetta.rosetta.core.pose.full_model_info) figure_out_fixed_domain_map() (in module pyrosetta.rosetta.core.import_pose) figure_out_motif_mode() (in module pyrosetta.rosetta.core.import_pose) figure_out_moving_chain_break_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_moving_chain_breaks() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_moving_cutpoints_closed() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_moving_cutpoints_closed_from_moving_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_moving_partition_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) figure_out_moving_partition_res_for_jump() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_moving_partition_res_for_suite() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_moving_rna_chain_breaks() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) figure_out_neighbors() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) figure_out_pose_domain_map() (in module pyrosetta.rosetta.core.pose.full_model_info) figure_out_pose_domain_map_const() (in module pyrosetta.rosetta.core.pose.full_model_info) figure_out_protein_modeling_info() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) figure_out_reasonable_rna_fold_tree() (in module pyrosetta.rosetta.core.pose.rna) figure_out_rebuild_bulge_mode() (in module pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters) figure_out_reference_res_for_jump() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) figure_out_reference_res_for_suite() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_repackable_residues() (in module pyrosetta.rosetta.core.pack) figure_out_residue_numbers_from_line() (in module pyrosetta.rosetta.core.io.silent) (pyrosetta.rosetta.core.io.silent.SilentStruct method) figure_out_root_and_moving_partition_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_root_partition_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_sample_both_sugar_base_rotamer() (in module pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters) figure_out_sample_res() (in module pyrosetta.rosetta.core.import_pose) figure_out_secstruct() (in module pyrosetta.rosetta.core.pose.rna) figure_out_segment_ids_from_line() (pyrosetta.rosetta.core.io.silent.SilentStruct method) figure_out_stepwise_movemap() (in module pyrosetta.rosetta.protocols.stepwise.modeler.movemap) figure_out_working_interface_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler.packer) figure_out_working_res() (in module pyrosetta.rosetta.core.import_pose) fij() (pyrosetta.rosetta.core.scoring.RDC method) file() (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) file_basename() (in module pyrosetta.rosetta.utility) (in module pyrosetta.rosetta.utility.file) file_contents() (in module pyrosetta.rosetta.utility) file_delete() (in module pyrosetta.rosetta.utility.file) file_exists() (in module pyrosetta.rosetta.utility.file) file_extension() (in module pyrosetta.rosetta.utility.file) file_full_path() (in module pyrosetta.rosetta.protocols.toolbox) file_is_atom_tree_diff() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) file_name() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) file_read() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) file_reading_token() (pyrosetta.rosetta.protocols.loops.Loops method) file_size() (in module pyrosetta.rosetta.utility.file) FileContentsMap (class in pyrosetta.rosetta.utility.io) FileJobOutputter (class in pyrosetta.rosetta.protocols.jd2) FileListResourceLocator (class in pyrosetta.rosetta.basic.resource_manager.locator) FileListResourceLocatorCreator (class in pyrosetta.rosetta.basic.resource_manager.locator) FileName (class in pyrosetta.rosetta.utility.file) filename() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ozstream method) FileOption (class in pyrosetta.rosetta.utility.options) FileOptionKey (class in pyrosetta.rosetta.utility.options) FileStream (class in pyrosetta.rosetta.basic.resource_manager.locator) FileSystemResourceLocator (class in pyrosetta.rosetta.basic.resource_manager.locator) FileSystemResourceLocatorCreator (class in pyrosetta.rosetta.basic.resource_manager.locator) FileType (class in pyrosetta.rosetta.core.import_pose) filetype() (in module pyrosetta.rosetta.protocols.cluster.calibur) FileVectorOption (class in pyrosetta.rosetta.utility.options) FileVectorOptionKey (class in pyrosetta.rosetta.utility.options) fill() (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) fill_A_line() (in module pyrosetta.rosetta.protocols.scoring.methods.pcs) (in module pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) (in module pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) (in module pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) (in module pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) fill_A_line_fast() (in module pyrosetta.rosetta.protocols.scoring.methods.pcs2) fill_A_line_slow() (in module pyrosetta.rosetta.protocols.scoring.methods.pcs2) fill_CA_coords() (in module pyrosetta.rosetta.protocols.toolbox) fill_data() (in module pyrosetta.rosetta.protocols.recces) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) fill_energy_map() (pyrosetta.rosetta.core.scoring.EnergyEdge method) fill_f1_f2() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) fill_from_string() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) fill_from_string_cs() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) fill_from_string_residue_depth_version1() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) fill_from_string_version1() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) fill_grid_with_backbone_heavyatom_spheres() (in module pyrosetta.rosetta.protocols.match) fill_grid_with_residue_heavyatom_spheres() (in module pyrosetta.rosetta.protocols.match) fill_grid_with_residue_spheres() (in module pyrosetta.rosetta.protocols.match) fill_h2o_hbond_set() (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) fill_hbond_bb_pair_score_dssp() (in module pyrosetta.rosetta.core.scoring.dssp) fill_hbond_set() (in module pyrosetta.rosetta.core.scoring.hbonds) fill_hbond_set_by_AHdist_threshold() (in module pyrosetta.rosetta.core.scoring.hbonds) fill_ideal_xyz_from_icoor() (pyrosetta.rosetta.core.chemical.ResidueType method) fill_in_default_jump_atoms() (in module pyrosetta.rosetta.core.pose.rna) fill_in_gaps() (in module pyrosetta.rosetta.protocols.frags) fill_intra_res_hbond_set() (in module pyrosetta.rosetta.core.scoring.hbonds) fill_jobs() (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) fill_missing_atoms() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) fill_mutations_list() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) fill_neighbor_residues() (in module pyrosetta.rosetta.core.select) fill_non_loop_cst_set() (in module pyrosetta.rosetta.protocols.forge.methods) fill_other_struct_list() (pyrosetta.rosetta.core.io.silent.SilentStruct method) fill_pose() (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) fill_rna_data_info() (pyrosetta.rosetta.core.io.rna.RNA_DataReader method) fill_rotamer_vector() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) fill_solution() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) fill_struct() (pyrosetta.rosetta.core.io.silent.SilentStruct method) fill_struct_with_residue_numbers() (pyrosetta.rosetta.core.io.silent.SilentStruct method) fill_struct_with_submotif_info_list() (pyrosetta.rosetta.core.io.silent.SilentStruct method) fill_template_frames_from_pdb() (in module pyrosetta.rosetta.core.fragment) fill_tenA_neighbor_residues() (in module pyrosetta.rosetta.core.select) fill_upstream_children_res_and_tips() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) fill_vdw_cached_rep_screen_info_from_command_line() (in module pyrosetta.rosetta.protocols.scoring) fill_vdw_cached_rep_screen_info_from_options() (in module pyrosetta.rosetta.protocols.scoring) FillAUTOTaskOperation (class in pyrosetta.rosetta.core.pack.task.operation) fillTargetPockets() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) Filter (class in pyrosetta.rosetta.protocols.pose_selectors) filter() (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) filter_acceptor_ligands() (in module pyrosetta.rosetta.protocols.magnesium) filter_by_constraints_energy_asymmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) filter_by_constraints_energy_symmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) filter_by_lj() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) filter_by_sidechain_distance_asymmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) filter_by_sidechain_distance_symmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) filter_loop_neighbors_by_distance() (in module pyrosetta.rosetta.protocols.loops) filter_max_bend() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) filter_max_dist() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) filter_max_orthoangle() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) filter_max_planeangle() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) filter_max_twist() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) filter_min_bend() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) filter_min_dist() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) filter_min_orthoangle() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) filter_min_planeangle() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) filter_min_twist() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) filter_motifs() (in module pyrosetta.rosetta.core.scoring.motif) filter_name() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) filter_native_big_bins() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) filter_neighbors_by_distance() (in module pyrosetta.rosetta.core.select) filter_on() (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) filter_out_high() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) filter_out_low() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) filter_structs() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) filter_type (class in pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter) FilterCollection (class in pyrosetta.rosetta.protocols.filters) FilterCreator (class in pyrosetta.rosetta.protocols.filters) filtered_base_axis_array() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) filtered_base_pair_array() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) filtered_base_stack_array() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) filtered_base_stack_axis_array() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) filtered_base_stagger_array() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) FilteredSolutions (class in pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers) FilterReportAsPoseExtraScoresMover (class in pyrosetta.rosetta.protocols.moves) FilterReporter (class in pyrosetta.rosetta.protocols.pose_reporters) FilterReporterMover (class in pyrosetta.rosetta.protocols.moves) filters() (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) FilterStructs (class in pyrosetta.rosetta.protocols.flxbb) FilterStructs_Packstat (class in pyrosetta.rosetta.protocols.flxbb) FilterStructs_TotalCharge (class in pyrosetta.rosetta.protocols.flxbb) final_cleanup() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) final_design_min() (in module pyrosetta.rosetta.protocols.ncbb) final_frlx_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) final_pose() (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) final_repack() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) Finalize() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) finalize() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) finalize_after_derivatives() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) finalize_after_minimizing() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) finalize_batch() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) finalize_claims() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) finalize_compound_records() (pyrosetta.rosetta.core.io.HeaderInformation method) finalize_experimental_technique_records() (pyrosetta.rosetta.core.io.HeaderInformation method) finalize_keyword_records() (pyrosetta.rosetta.core.io.HeaderInformation method) finalize_parse() (pyrosetta.rosetta.core.io.HeaderInformation method) finalize_scoring() (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) finalize_simulation() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) finalize_total_energy() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) FinalizeAromatic() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) finalized() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) finalized_energies() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) FinalizeUnhybridized() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) find() (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) find_attach_pt() (in module pyrosetta.rosetta.protocols.ligand_docking) find_automatically() (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) find_basepairs() (in module pyrosetta.rosetta.core.scoring.dna) (in module pyrosetta.rosetta.protocols.dna) find_best_match() (in module pyrosetta.rosetta.core.chemical) find_bonds_in_rings() (in module pyrosetta.rosetta.core.chemical) find_bound_waters_that_are_daughters_in_fold_tree() (in module pyrosetta.rosetta.protocols.magnesium) find_cache_file() (in module pyrosetta.rosetta.basic.database) find_char_location_in_string() (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) find_chi_bonds() (in module pyrosetta.rosetta.core.chemical) find_chunk() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) find_closest() (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) find_closest_atom() (in module pyrosetta.rosetta.protocols.metal_interface) Find_Closest_Intersect_SQ() (in module pyrosetta.rosetta.protocols.pockets) find_common_intersection_atoms() (in module pyrosetta.rosetta.core.scoring.power_diagram) find_connected_components() (in module pyrosetta.rosetta.utility.graph) find_connecting_jump() (in module pyrosetta.rosetta.protocols.forge.methods) find_cutpoint() (in module pyrosetta.rosetta.protocols.forge.methods) find_cutpoint_from_secondary_structure() (in module pyrosetta.rosetta.protocols.fold_from_loops.utils) find_cutpoint_variants() (in module pyrosetta.rosetta.core.scoring.methods) find_database_path() (in module pyrosetta.rosetta.basic.database) find_design_interface() (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) find_design_interface_arg_sweep() (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) find_downstream_connection_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) find_edge() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) find_energy_edge() (pyrosetta.rosetta.core.scoring.EnergyGraph method) find_existing_residues() (in module pyrosetta.rosetta.protocols.evaluation) find_filter_or_die() (in module pyrosetta.rosetta.protocols.moves) find_first_interface_residue() (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) find_first_not_of() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_first_of() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_glycan_sequence_file() (in module pyrosetta.rosetta.core.chemical.carbohydrates) find_hash_edge() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) find_HBondResStruct() (in module pyrosetta.rosetta.protocols.hbnet) find_hbonds_in_residue_pair() (in module pyrosetta.rosetta.core.pack.hbonds) find_helices_over_length() (in module pyrosetta.rosetta.protocols.aa_composition) find_hits() (pyrosetta.rosetta.protocols.match.Matcher method) find_in_pose_if_missing_from_header() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) find_index_in_other_pose_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) find_intersections() (in module pyrosetta.rosetta.core.scoring.power_diagram) find_jump_number_at_suite() (in module pyrosetta.rosetta.protocols.stepwise.modeler) find_jump_rec() (in module pyrosetta.rosetta.protocols.denovo_design) find_key_cl() (pyrosetta.rosetta.utility.options.OptionCollection method) find_key_file() (pyrosetta.rosetta.utility.options.OptionCollection method) find_last() (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_last_non_whitespace() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_last_not_of() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_last_of() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_last_whitespace() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_length() (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) find_ligands() (in module pyrosetta.rosetta.protocols.flxbb) find_lowest_constraint_energy_residue() (in module pyrosetta.rosetta.protocols.protein_interface_design) find_max_r() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) find_metalbinding_atoms() (in module pyrosetta.rosetta.core.util) find_metalbinding_atoms_for_complex() (in module pyrosetta.rosetta.core.util) find_metalbinding_atoms_helper() (in module pyrosetta.rosetta.core.util) find_min_xyz() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) find_minimization_edge() (pyrosetta.rosetta.core.scoring.MinimizationGraph method) find_mover_or_die() (in module pyrosetta.rosetta.protocols.moves) find_nbr_dist() (in module pyrosetta.rosetta.core.chemical) find_nearest_disulfide() (in module pyrosetta.rosetta.protocols.rosetta_scripts) find_nearest_res() (in module pyrosetta.rosetta.protocols.rosetta_scripts) find_nearest_residue() (in module pyrosetta.rosetta.protocols.protein_interface_design) find_nearest_residue_to_coord() (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) find_neighbors() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) find_neighbors_restricted() (in module pyrosetta.rosetta.core.conformation) find_new_jump_residue() (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) find_new_symmetric_jump_residues() (in module pyrosetta.rosetta.core.pose.symmetry) find_next_vertex_with_smallest_dist() (in module pyrosetta.rosetta.core.scoring.power_diagram) find_non_protein_chunks() (in module pyrosetta.rosetta.protocols.loops) find_non_whitespace() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_num_scattering_atoms() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) find_orientations_and_lengths() (in module pyrosetta.rosetta.protocols.denovo_design.components) find_overlap() (in module pyrosetta.rosetta.core.pack) find_pairing() (in module pyrosetta.rosetta.protocols.fldsgn.filters) find_pairing_idx() (in module pyrosetta.rosetta.protocols.fldsgn.filters) find_peptide_attach_pt() (in module pyrosetta.rosetta.protocols.ligand_docking) find_pitch() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) find_possible_orders() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) find_regions_with_minimum_size() (in module pyrosetta.rosetta.protocols.nonlocal) find_relevant_connections_onersd() (in module pyrosetta.rosetta.core.scoring.methods) find_residue_max_radii() (in module pyrosetta.rosetta.core.pack) find_rosettascript_tag() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) find_satisfying_interactions_with_background() (in module pyrosetta.rosetta.core.pack.hbonds) find_seqpos_of_saccharides_child_residue_at() (in module pyrosetta.rosetta.core.conformation.carbohydrates) find_seqpos_of_saccharides_mainchain_child() (in module pyrosetta.rosetta.core.conformation.carbohydrates) find_seqpos_of_saccharides_parent_residue() (in module pyrosetta.rosetta.core.conformation.carbohydrates) find_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) find_SilentStructOPs (class in pyrosetta.rosetta.protocols.wum) find_start_of_next_interface_region() (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) find_stop_of_this_interface_region() (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) find_symmetric_basejump_anchor() (in module pyrosetta.rosetta.core.pose.symmetry) find_unconnected_residues() (in module pyrosetta.rosetta.protocols.ligand_docking) find_weights_file() (in module pyrosetta.rosetta.core.scoring) find_whitespace() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) findClusters() (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) findClustersByExemplars() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) findExemplars() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) findLoopFromDensity() (in module pyrosetta.rosetta.protocols.electron_density) findPockets() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) FindPossibleAtomTypesForAtom() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) findPSP() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) findSampling() (in module pyrosetta.rosetta.core.scoring.electron_density) (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) findSampling5() (in module pyrosetta.rosetta.core.scoring.electron_density) (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) findSPS() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) findUU() (in module pyrosetta.rosetta.numeric.model_quality) finer_sampling_at_chain_closure() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) FingerprintMultifunc (class in pyrosetta.rosetta.protocols.pockets) finish_pose() (pyrosetta.rosetta.core.io.silent.SilentStruct method) finished() (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) finished_simulation() (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) finite() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) first_adjacent_heavy_atom() (pyrosetta.rosetta.core.conformation.Residue method) first_base_atom() (in module pyrosetta.rosetta.core.chemical.rna) first_base_atom_index() (in module pyrosetta.rosetta.core.chemical.rna) first_connected_resonance() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) first_node_is_the_acceptor() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond method) first_residue() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) first_residue_index() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) first_sidechain_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) first_sidechain_hydrogen() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) fit_centered_coords() (in module pyrosetta.rosetta.protocols.toolbox) fit_layer_lines_with_splines() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) fitness() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) fitness_pbest() (pyrosetta.rosetta.core.optimization.Particle method) fitness_valid() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) fitnessCostPerATP() (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) FitSimpleHelixMultiFunc (class in pyrosetta.rosetta.protocols.helical_bundle) fiveprime_cap() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) fix_bfactorsH() (in module pyrosetta.rosetta.core.scoring.cryst) fix_bfactorsMissing() (in module pyrosetta.rosetta.core.scoring.cryst) fix_disulfides() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) fix_glycan_order() (in module pyrosetta.rosetta.core.io) FIX_HIS_TAUTOMER (class in pyrosetta.rosetta.core.pack.task) fix_his_tautomer() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) fix_pdbinfo_damaged_by_insertion() (in module pyrosetta.rosetta.core.pose) fix_protein_jump_atom() (in module pyrosetta.rosetta.protocols.stepwise.modeler) fix_reference_energies() (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) fix_sugar_coords() (in module pyrosetta.rosetta.core.pose.rna) fix_tag_suffix() (in module pyrosetta.rosetta.protocols.toolbox) fix_up_jump_atoms() (in module pyrosetta.rosetta.protocols.stepwise.modeler) fix_up_jump_atoms_and_residue_type_variants() (in module pyrosetta.rosetta.protocols.stepwise.modeler) fix_up_residue_type_variants() (in module pyrosetta.rosetta.core.pose) fix_up_residue_type_variants_at_strand_beginning() (in module pyrosetta.rosetta.core.pose) fix_up_residue_type_variants_at_strand_end() (in module pyrosetta.rosetta.core.pose)

fix_with_coord_cst() (in module pyrosetta.rosetta.protocols.loops) fix_worst_bad_ramas() (in module pyrosetta.rosetta.protocols.relax) fixed() (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) fixed_dist() (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) fixed_domain_map() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) fixed_energies() (pyrosetta.rosetta.core.scoring.MinimizationGraph method) fixed_energy_terms() (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) fixed_size() (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) FixedOffsetPivots (class in pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers) FixedOffsetsPivots (class in pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers) FixedPivots (class in pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers) FixedTemperatureController (class in pyrosetta.rosetta.protocols.canonical_sampling) fixEigenvector() (in module pyrosetta.rosetta.numeric.model_quality) fixH() (in module pyrosetta.rosetta.protocols.relax) fixResidue() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) fixup_magnesiums() (in module pyrosetta.rosetta.protocols.magnesium) fixup_patches() (in module pyrosetta.rosetta.core.chemical) flag_file() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) flag_for_calculation() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) flags() (pyrosetta.rosetta.basic.Tracer method) flanking_left_aa() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) flanking_left_nres() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) flanking_left_ss() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) flanking_right_aa() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) flanking_right_nres() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) flanking_right_ss() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) flexbb() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) FlexBBMeanField (class in pyrosetta.rosetta.protocols.mean_field) flip_atom_xyz() (in module pyrosetta.rosetta.core.io.pose_from_sfr) flip_HNQ() (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) flip_subset() (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) flip_upstream_downstream_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) FlipMover (class in pyrosetta.rosetta.protocols.membrane) FlipMoverCreator (class in pyrosetta.rosetta.protocols.membrane) float_ambiguity() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) float_label() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) float_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) FloatingResonance (class in pyrosetta.rosetta.protocols.noesy_assign) flood_fill3D() (in module pyrosetta.rosetta.protocols.sic_dock) FloppyTailMover (class in pyrosetta.rosetta.protocols.floppy_tail) flush() (pyrosetta.logging_support.PythonLoggingSink method) (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerImpl method) (pyrosetta.rosetta.basic.YamlEmitter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.output.ResultOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) flush_all_channels() (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerImpl method) flush_finalize() (pyrosetta.rosetta.utility.io.ozstream method) FlxbbDesign (class in pyrosetta.rosetta.protocols.flxbb) FlxbbDesign_main() (in module pyrosetta.rosetta.protocols.flxbb) FlxbbDesignPack (class in pyrosetta.rosetta.protocols.flxbb) fmt_real() (in module pyrosetta.rosetta.utility) fname() (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) focused_edge() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) fold() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) fold_in_rb_deltas() (pyrosetta.rosetta.core.kinematics.Jump method) fold_label_resonance() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) fold_proton_resonance() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) fold_tree() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) fold_tree_from_loops() (in module pyrosetta.rosetta.protocols.forge.methods) (in module pyrosetta.rosetta.protocols.loops) fold_tree_from_pose() (in module pyrosetta.rosetta.protocols.forge.methods) fold_tree_io() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) FoldConstraints (class in pyrosetta.rosetta.protocols.abinitio) FoldConstraints.StageID (class in pyrosetta.rosetta.protocols.abinitio) foldInChanges() (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) FoldTree (class in pyrosetta.rosetta.core.kinematics) foldTree() (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) foldtree_string() (pyrosetta.rosetta.core.io.StructFileRep method) FoldTreeFromFoldGraphMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) FoldTreeRequest (class in pyrosetta.rosetta.protocols.loop_modeling) foldtype_from_name() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) foldtype_from_spairs() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) follow_edge() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) foo_all() (in module pyrosetta.rosetta.utility.py) foo_all_sp() (in module pyrosetta.rosetta.utility.py) foo_int() (pyrosetta.rosetta.utility.py.Base method) foo_string() (pyrosetta.rosetta.utility.py.Base method) foo_value() (pyrosetta.rosetta.utility.py.Base method) foo_value_sp() (pyrosetta.rosetta.utility.py.Base method) force_aa_neighbors_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) force_all_aa_neighbors_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) force_bitflip() (pyrosetta.rosetta.core.io.silent.SilentStruct method) force_centroid_interaction() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) force_const() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) force_fold_tree() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) force_job_purging() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) force_nbr_atom_orient() (pyrosetta.rosetta.core.chemical.ResidueType method) force_phosphate_instantiation() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) ForceDisulfidesMover (class in pyrosetta.rosetta.protocols.calc_taskop_movers) form_disulfide() (in module pyrosetta.rosetta.core.conformation) form_disulfide_helper() (in module pyrosetta.rosetta.core.conformation) formal_charge() (pyrosetta.rosetta.core.chemical.Atom method) formatted_icoord_tree() (in module pyrosetta.rosetta.core.chemical) FormFactorManager (class in pyrosetta.rosetta.core.scoring.saxs) forward_connections() (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) FourAtomsConstraintData (class in pyrosetta.rosetta.protocols.frag_picker.scores) FourPointsFunc (class in pyrosetta.rosetta.core.scoring.func) frac_atoms_within() (in module pyrosetta.rosetta.protocols.ligand_docking) fract_property_penalty() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) frag_files() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) frag_id() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) frag_libs() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) frag_set_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.FragSetLoader method) frag_sizes() (pyrosetta.rosetta.protocols.frags.FragLib method) FragInsertAndAlignMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) FragLib (class in pyrosetta.rosetta.protocols.frags) fragment() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) fragment_as_pose() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) fragment_contacts() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) fragment_ptr() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) fragment_set_slice() (in module pyrosetta.rosetta.core.fragment) FragmentAllAtomCrmsd (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentCandidate (class in pyrosetta.rosetta.protocols.frag_picker) FragmentChunkCrms (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentCrmsd (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentCrmsdResDepth (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentDME (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentJumpClaimer (class in pyrosetta.rosetta.protocols.topology_broker) FragmentLibraryManager (class in pyrosetta.rosetta.core.fragment.picking_old) FragmentMover (class in pyrosetta.rosetta.protocols.simple_moves) FragmentPerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) FragmentPicker (class in pyrosetta.rosetta.protocols.frag_picker) fragments() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.nonlocal.Policy method) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy method) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) fragments_for_permutation() (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) fragments_for_permutation_take_X_from_pose() (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) fragments_id() (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) FragmentSampler (class in pyrosetta.rosetta.protocols.abinitio) FragmentScoreFilter (class in pyrosetta.rosetta.protocols.frag_picker) FragmentScoreManager (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentScoreMap (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentScoringMethod (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentSelectingRule (class in pyrosetta.rosetta.protocols.frag_picker) FragmentSetLoader (class in pyrosetta.rosetta.core.fragment) FragmentSetLoaderCreator (class in pyrosetta.rosetta.core.fragment) frags_per_pos() (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector method) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector method) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector method) FragSet (class in pyrosetta.rosetta.core.fragment) FragSetLoader (class in pyrosetta.rosetta.protocols.parser) Frame (class in pyrosetta.rosetta.core.fragment) frame() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) frames() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) framework_dependant_clusters() (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) framework_dependant_mutations() (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) framework_dependant_positions() (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) free_dof_options() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) free_rsd() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) FreePeptide (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover) FreePeptideMover (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers) freeze() (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) freeze_sugar_torsions() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) freq() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) frequency_in_taboo_map() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) fresh_instance() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) from_bond_cst() (pyrosetta.rosetta.core.kinematics.Jump method) from_four_points() (pyrosetta.rosetta.core.kinematics.Stub method) from_other_chains() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) from_remark() (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) from_same_chain() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) from_span() (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) from_span_positive_z() (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) from_stubs() (pyrosetta.rosetta.core.kinematics.Jump method) front() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) Fstring (class in pyrosetta.rosetta.ObjexxFCL) Fstring_of() (in module pyrosetta.rosetta.ObjexxFCL) Fsubstring (class in pyrosetta.rosetta.ObjexxFCL) ft_mover() (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) ftoa() (in module pyrosetta.rosetta.protocols.sparta) full_cache_name() (in module pyrosetta.rosetta.basic.database) full_definition() (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) full_hit() (in module pyrosetta.rosetta.protocols.match) full_length_rmsd_over_residue_list() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) full_model_info_defined() (in module pyrosetta.rosetta.core.pose.full_model_info) full_model_info_into_pose() (pyrosetta.rosetta.core.io.silent.SilentStruct method) full_model_parameter_type_from_string() (in module pyrosetta.rosetta.core.pose.full_model_info) full_model_parameters() (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) full_model_size() (in module pyrosetta.rosetta.core.pose.full_model_info) full_name() (in module pyrosetta.rosetta.basic.database) full_sequence() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) full_to_sub() (in module pyrosetta.rosetta.core.pose.full_model_info) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) fullatom_scorefxn() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) fullatom_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) FullAtomRNA_Fragments (class in pyrosetta.rosetta.core.fragment.rna) FullModelInfo (class in pyrosetta.rosetta.core.pose.full_model_info) FullModelParameterType (class in pyrosetta.rosetta.core.pose.full_model_info) Func (class in pyrosetta.rosetta.core.scoring.func) func() (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.protocols.moves.GeometricFunc method) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc method) func_() (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) function_tag() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method)

G

G() (in module pyrosetta.rosetta.ObjexxFCL.format) gamma() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.CSA method) gamma_aform() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gap_solved() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) GapCloser (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover) GapSolutionPicker (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers) gasteiger_atom_type() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.ResidueType method) gasteiger_atom_type_set() (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) gasteiger_atom_typeset() (pyrosetta.rosetta.core.chemical.ResidueType method) GasteigerAtomTypeData (class in pyrosetta.rosetta.core.chemical.gasteiger) GasteigerAtomTypeData.AtomicOrbitalTypes (class in pyrosetta.rosetta.core.chemical.gasteiger) GasteigerAtomTypeData.HybridOrbitalType (class in pyrosetta.rosetta.core.chemical.gasteiger) GasteigerAtomTypeData.PiContributionType (class in pyrosetta.rosetta.core.chemical.gasteiger) GasteigerAtomTypeData.Properties (class in pyrosetta.rosetta.core.chemical.gasteiger) GasteigerAtomTypeData.TypeDifference (class in pyrosetta.rosetta.core.chemical.gasteiger) GasteigerAtomTypeSet (class in pyrosetta.rosetta.core.chemical.gasteiger) gather_coords() (in module pyrosetta.rosetta.protocols.comparative_modeling) gaussian() (in module pyrosetta.rosetta.numeric.random) (pyrosetta.rosetta.numeric.random.RandomGenerator method) gaussian_deriv() (in module pyrosetta.rosetta.core.scoring.constraints) gaussian_jump_move() (in module pyrosetta.rosetta.protocols.rigid) gaussian_move() (pyrosetta.rosetta.core.kinematics.Jump method) gaussian_move_single_rb() (pyrosetta.rosetta.core.kinematics.Jump method) gaussian_parameter_set_alpha() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_beta() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_chi_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_chi_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_delta_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_delta_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_epsilon_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_epsilon_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_gamma() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_nu1_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_nu1_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_nu2_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_nu2_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_zeta_alpha_ap() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_zeta_alpha_sc_minus() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_zeta_alpha_sc_plus() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_random_xform() (in module pyrosetta.rosetta.numeric.random) gaussian_stdev() (in module pyrosetta.rosetta.protocols.recces) GaussianFunc (class in pyrosetta.rosetta.core.scoring.func) GaussianParameter (class in pyrosetta.rosetta.core.chemical.rna) GaussianRBSegmentMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) gcount() (pyrosetta.rosetta.utility.io.izstream method) gdtha() (in module pyrosetta.rosetta.core.scoring) gdtsc() (in module pyrosetta.rosetta.core.scoring) GenBornPoseInfo (class in pyrosetta.rosetta.core.scoring) GenBornPotential (class in pyrosetta.rosetta.core.scoring) GenBornResidueInfo (class in pyrosetta.rosetta.core.scoring) GenBornRotamerSetInfo (class in pyrosetta.rosetta.core.scoring) general() (in module pyrosetta.rosetta.ObjexxFCL.format) general_base_pair_step_library() (pyrosetta.rosetta.core.import_pose.libraries.RNA_LibraryManager method) general_set_phi() (in module pyrosetta.rosetta.protocols.generalized_kinematic_closure) general_set_psi() (in module pyrosetta.rosetta.protocols.generalized_kinematic_closure) GeneralAntibodyModeler (class in pyrosetta.rosetta.protocols.antibody.design) GeneralEvent (class in pyrosetta.rosetta.core.conformation.signals) (class in pyrosetta.rosetta.core.pose.signals) GeneralizedKICfilter (class in pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter) GeneralizedKICperturber (class in pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber) GeneralizedKICselector (class in pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector) generate_atom_positions() (in module pyrosetta.rosetta.protocols.helical_bundle) generate_batch() (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) generate_bb_coordinate_constraints() (in module pyrosetta.rosetta.protocols.relax) generate_beta_database_test() (in module pyrosetta.rosetta.protocols.stepwise.sampler.protein) generate_binary_score_file() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) generate_centroid_constraints() (in module pyrosetta.rosetta.protocols.hybridization) generate_claims() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) generate_constraint_files() (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) generate_constraints() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) generate_edges() (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) generate_empty_jump_frame() (in module pyrosetta.rosetta.protocols.jumping) generate_fullatom_constraints() (in module pyrosetta.rosetta.protocols.hybridization) generate_human_readable_documentation() (in module pyrosetta.rosetta.utility.xsd_util) generate_human_readable_recursive() (in module pyrosetta.rosetta.utility.xsd_util) generate_human_readable_summary() (in module pyrosetta.rosetta.utility.xsd_util) generate_insert_map() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) generate_inverse_rotamer_constraints() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) generate_jump_frags() (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) generate_jump_frame() (in module pyrosetta.rosetta.protocols.jumping) generate_key() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) generate_mover_and_apply_to_pose() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) generate_mover_and_apply_to_pose_xml_string() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) generate_mover_for_protocol() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) generate_mover_from_pose() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) generate_N2C_cyclic_peptide_protein_complex() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) generate_nonstandard_residue_set() (in module pyrosetta) generate_pose_specific_data() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) generate_prob() (in module pyrosetta.rosetta.core.io.external) generate_property_to_string_vector() (pyrosetta.rosetta.core.chemical.ResidueProperties method) generate_relax_from_cmd() (in module pyrosetta.rosetta.protocols.relax) generate_remodel_constraints() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) generate_replacement_restype() (in module pyrosetta.rosetta.core.util) generate_resfile_from_pdb() (in module pyrosetta.toolbox) (in module pyrosetta.toolbox.generate_resfile) generate_resfile_from_pose() (in module pyrosetta.toolbox) (in module pyrosetta.toolbox.generate_resfile) generate_secstruct_for_length() (in module pyrosetta.rosetta.protocols.denovo_design.architects) generate_seqmap_from_poses() (in module pyrosetta.rosetta.protocols.constraint_generator) generate_sequence_claims() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) generate_shannon_points() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) generate_sub_fragment() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) generate_sub_frame() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) generate_tag_given_options() (in module pyrosetta.rosetta.utility.xsd_util) generate_targets_and_inverse_rotamers() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) generate_task_op_all_cdr_design() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) generate_task_op_cdr_design() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) generate_task_op_cdr_profiles() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) generate_taskfactory_and_add_task_awareness() (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) generate_tf_seq_design() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) generate_tf_seq_design_graft_design() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) generate_unique_name() (in module pyrosetta.rosetta.protocols.ligand_docking) generate_unique_structure_id() (in module pyrosetta.rosetta.protocols.wum) generate_variant_to_string_vector() (pyrosetta.rosetta.core.chemical.ResidueProperties method) generates_aa() (pyrosetta.rosetta.core.chemical.Patch method) generates_base_residue() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.RenameAtom method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.Set_AA method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) generates_interchangeability_group() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.RenameAtom method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.Set_AA method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) generates_name3() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.RenameAtom method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.Set_AA method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) generates_new_name3() (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) generates_patched_residue_type_with_interchangeability_group() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) generates_patched_residue_type_with_name3() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) generates_primary_hits() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) GenerateStoredRBConfs (class in pyrosetta.rosetta.protocols.enzdes) generators() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) GenericBondedPotential (class in pyrosetta.rosetta.core.scoring) GenericJobInputter (class in pyrosetta.rosetta.protocols.comparative_modeling) GenericRemodelConstraintGenerator (class in pyrosetta.rosetta.protocols.forge.remodel) GenericSimulatedAnnealer (class in pyrosetta.rosetta.protocols.monte_carlo) geom_cst_id() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) geom_sol_interres_path_distance_cutoff() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) geom_sol_intrares_path_distance_cutoff() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) GeometricFunc (class in pyrosetta.rosetta.protocols.moves) GeometricSolvationFeaturesCreator (class in pyrosetta.rosetta.protocols.features) GeometrySecMatchRPE (class in pyrosetta.rosetta.protocols.match.downstream) GeomSampleInfo (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) get() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) (pyrosetta.rosetta.protocols.neighbor.Neighborhood method) (pyrosetta.rosetta.protocols.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborsByDistanceCalculator method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) get_2way_orientation() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) get_3_letter_codes_from_peptide_consensus_sequence() (in module pyrosetta.rosetta.core.enzymes) get_5_ss_models_from_db() (in module pyrosetta.rosetta.protocols.legacy_sewing) get_6D_trans_rot_potential_evaluator() (in module pyrosetta.rosetta.core.scoring.loop_graph) get_A() (in module pyrosetta.rosetta.core.scoring.electron_density) (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) get_a_axis() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_aa_submatrix_energies_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) get_ab_cdr_bfactors() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper method) get_ab_design_dock_high_scorefxn() (in module pyrosetta.rosetta.protocols.antibody.design) get_ab_design_dock_low_scorefxn() (in module pyrosetta.rosetta.protocols.antibody.design) get_ab_design_global_scorefxn() (in module pyrosetta.rosetta.protocols.antibody.design) get_ab_design_min_scorefxn() (in module pyrosetta.rosetta.protocols.antibody.design) get_ab_OCDs() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper method) get_ab_region_outliers() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper method) get_abego() (in module pyrosetta.rosetta.core.sequence) get_abego_string() (pyrosetta.rosetta.core.sequence.ABEGOManager method) get_abort_on_failed_loop() (pyrosetta.rosetta.protocols.LoopRebuild method) get_accept_aborted_loops() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) get_add_constraints() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) get_additional_output() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) get_additional_task_operarations() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) get_adjacent_heavy_atoms() (pyrosetta.rosetta.core.conformation.Residue method) get_akash_dyepos() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_al_tensor_max_z() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) get_al_tensor_trace() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) get_alignment_domain() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) get_all_born_radii() (pyrosetta.rosetta.core.scoring.GenBornPotential method) get_all_cdrs() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_all_cdrs_present() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_all_channels_string() (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerImpl method) get_all_comments() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.core.io.silent.SilentStruct method) get_all_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) get_all_data() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_all_exemplars() (pyrosetta.rosetta.protocols.cluster.APCluster method) get_all_features_names() (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) get_all_function_names() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) get_all_glycans_and_neighbor_res_task_factory() (in module pyrosetta.rosetta.protocols.carbohydrates) get_all_graft_permutations() (in module pyrosetta.rosetta.protocols.antibody.design) get_all_jacobians() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) get_all_loops_closed() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) get_all_loops_definer_names() (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) get_all_per_residue_data() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_all_possible_water_sites() (in module pyrosetta.rosetta.core.pack) get_all_properties() (pyrosetta.rosetta.core.chemical.AtomType method) get_all_register_and_bulges() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) get_all_res_list() (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo) get_all_residues() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_all_residues_in_this_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_all_score_line_strings() (in module pyrosetta.rosetta.core.pose) get_all_scores() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) get_all_solutions() (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) get_all_types_with_variants_aa() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_all_types_with_variants_name1() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_all_types_with_variants_name3() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_all_working_moving_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_AllCDRs_in_loopsop() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_allow_anchor_repack() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_allowed_failure_before_extend() (pyrosetta.rosetta.protocols.LoopRebuild method) get_allowed_failure_before_stop() (pyrosetta.rosetta.protocols.LoopRebuild method) get_alpha_beta_models_from_db() (in module pyrosetta.rosetta.protocols.legacy_sewing) get_alt_score_() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) get_alternate_for_node() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) get_alternative_search_paths() (pyrosetta.rosetta.utility.io.izstream method) get_anchor_and_root_atoms() (in module pyrosetta.rosetta.core.conformation) get_anchor_atomno() (in module pyrosetta.rosetta.core.conformation) get_anchor_noise_constraints_mode() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_anchor_points_for_tmcom() (in module pyrosetta.rosetta.protocols.membrane) get_anchor_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) get_anchor_rsd() (in module pyrosetta.rosetta.core.import_pose) get_anchor_via_constraints() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_angle() (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) get_angle_cutoff() (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) get_angle_diffs() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) get_angle_max() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) get_angle_range() (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) get_angles() (in module pyrosetta.rosetta.core.scoring) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) get_angular_momentum_quantum_number() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) get_antibody_chain_ids() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_antibody_chain_string() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_antibody_chains() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_antibody_enum_manager() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_antibody_numbering() (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser method) get_antibody_numbering_info() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_antibody_sequence() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_antigen_chain_ids() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_antigen_chain_string() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_antigen_chains() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_antiparallel_weight() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) get_area_from_cycle() (in module pyrosetta.rosetta.core.scoring.power_diagram) get_argv() (pyrosetta.rosetta.utility.options.OptionCollection method) get_aro_residues_in_this_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_asymm_unit_fold_tree() (in module pyrosetta.rosetta.core.conformation.symmetry) get_asymmetric_pose_copy_from_symmetric_pose() (in module pyrosetta.rosetta.core.pose.symmetry) get_atom_bin() (in module pyrosetta.rosetta.core.pose.rna) get_atom_collision_radius() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) get_atom_coordinates() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) get_atom_coords_xyz() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) get_atom_counts() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) get_atom_index() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) get_atom_interaction_radius() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) get_atom_level_domain_map() (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) get_atom_name() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) get_atom_positions() (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) get_atom_radius() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) get_atom_sasa() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_atom_type_property() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_atom_weights() (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase method) get_atomic_number() (pyrosetta.rosetta.core.chemical.Element method) get_atomname() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) get_atomnames_size() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) get_atoms_ala() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_ala_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_arg() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_arg_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_asn() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_asn_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_asp() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_asp_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_cys() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_cys_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_gln() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_gln_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_glu() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_glu_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_gly() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_gly_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_his() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_his_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_ile() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_ile_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_leu() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_leu_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_lys() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_lys_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_met() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_met_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_phe() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_phe_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_pro() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_pro_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_ser() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_ser_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_thr() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_thr_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_trp() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_trp_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_tyr() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_tyr_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_val() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_val_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_attachment_point_string() (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) get_automorphic_RMSDs() (in module pyrosetta.rosetta.protocols.ligand_docking) get_average_cation_pi_ip_to_neutral_ip_ratio() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_average_cation_sigma_ip_to_neutral_ip_ratio() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_average_ip_change_cation_to_neutral() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_average_ip_change_neutral_to_anion() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_average_neutral_pi_ip_to_anion_ip_ratio() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_average_neutral_sigma_ip_to_anion_ip_ratio() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_avg_dis_CA_CA() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_avg_dis_strands() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_axis() (pyrosetta.rosetta.protocols.membrane.FlipMover method) get_b_axis() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_backbone_reference_frame() (in module pyrosetta.rosetta.core.pose.motif) get_backbone_reference_frame_atomids() (in module pyrosetta.rosetta.core.pose.motif) get_backbone_reference_frame_atomids_with_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_backbone_segments() (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) get_base_atom_name() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_base_backbone() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) get_base_base_atom_name() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_base_centroid() (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) get_base_centroid_and_rotation_matrix() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) get_base_coordinate_system() (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) get_base_doublet_orientation_from_LW() (in module pyrosetta.rosetta.core.pose.rna) get_base_pair_atoms() (in module pyrosetta.rosetta.core.chemical.rna) get_base_pair_params() (in module pyrosetta.rosetta.core.scoring.dna) get_base_pair_stub_slow() (in module pyrosetta.rosetta.core.scoring.dna) get_base_pairing_info() (in module pyrosetta.rosetta.core.pose.rna) get_base_pairing_list() (in module pyrosetta.rosetta.core.pose.rna) get_base_step_params() (in module pyrosetta.rosetta.core.scoring.dna) get_base_stub() (in module pyrosetta.rosetta.core.scoring.dna) get_base_type_cop() (pyrosetta.rosetta.core.chemical.ResidueType method) get_base_types_aa() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_base_types_name1() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_base_types_name3() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_basic_protein_sampler() (in module pyrosetta.rosetta.protocols.stepwise.sampler.protein) get_batch_id() (in module pyrosetta.rosetta.protocols.features) get_bb() (pyrosetta.rosetta.core.kinematics.MoveMap method) get_bb_atoms_for_residue() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) get_bb_ids() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_bb_range() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_bb_torsion() (in module pyrosetta.rosetta.core.pose) get_bbcsts() (in module pyrosetta.rosetta.protocols.protein_interface_design) get_best_neighboring_shift_RMSD_and_output_silent_file() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) get_bestpose() (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) get_beta_pairs() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) get_bias_sampling() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_big_bin() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) get_bin_and_pos() (pyrosetta.rosetta.protocols.match.VoxelSetIterator method) get_binary_name() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) get_binary_rna_silent_struct_safe() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) get_binary_rna_silent_struct_safe_wrapper() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) get_bins() (in module pyrosetta.rosetta.core.scoring.motif) get_bins_per_A2() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) get_boltzmann_temp() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) get_bond_length() (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) get_bool_idx() (in module pyrosetta.rosetta.core.scoring.rna.data) get_boolean_option() (in module pyrosetta.rosetta.basic.options) get_boolean_vector_option() (in module pyrosetta.rosetta.basic.options) get_bound_mut_pose() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) get_bound_wt_pose() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) get_branches() (pyrosetta.rosetta.core.kinematics.MoveMap method) get_branching_atoms2() (in module pyrosetta.rosetta.protocols.branch_angle) get_branching_residues() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_bridge_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) get_build_all_loops() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) get_build_attempts() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) get_buildingblock_and_neighbor_subs() (in module pyrosetta.rosetta.core.pose.symmetry) get_bump_check() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_bump_overlap_factor() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) get_bumpcheck_atom_count_for_residue() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) get_bumpcheck_atoms_for_residue() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) get_c_alpha_centroid() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_c_alpha_non_ellipsoid_centroid() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_c_axis() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_c_cyd_seqpos() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) get_ca_bfactors() (pyrosetta.rosetta.protocols.match.BfactorMPM method) get_CA_vectors() (in module pyrosetta.rosetta.core.scoring.dssp) get_CA_xyz() (pyrosetta.rosetta.core.io.silent.SilentStruct method) get_cacheable_cluster_data() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) get_calculator() (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) get_calculator_name() (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) get_candidate_i() (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair method) get_candidate_i_rank() (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair method) get_candidate_j() (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair method) get_candidate_j_rank() (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair method) get_candidates() (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) get_candidates_collector() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_carbohydrate_residues_and_tips_of_branch() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_carbohydrate_residues_of_branch() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_carbohydrate_tips_of_branch() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_cartesian_bonded_linear() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) get_cartesian_bonded_parameters() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) get_CB_Vecs_from_map() (in module pyrosetta.rosetta.protocols.sic_dock) get_CB_Vecs_from_pose() (in module pyrosetta.rosetta.protocols.sic_dock) get_ccd_closure_exist() (pyrosetta.rosetta.protocols.LoopRebuild method) get_cdr_bool_from_tag() (in module pyrosetta.rosetta.protocols.antibody) get_CDR_chain() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_CDR_cluster() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cdr_cluster() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher method) get_cdr_cluster_enum_manager() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_CDR_cluster_set() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cdr_design_options() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) get_CDR_end() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_CDR_end_PDB_num() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cdr_enum_for_cluster() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_CDR_in_loopsop() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_CDR_length() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_CDR_loop() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cdr_loop_with_overhang() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) get_cdr_loops() (in module pyrosetta.rosetta.protocols.antibody) get_CDR_loops() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cdr_loops() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) get_cdr_loops_with_overhang() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) get_CDR_name() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_CDR_name_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_CDR_sequence_with_stem() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cdr_set_options() (in module pyrosetta.rosetta.protocols.antibody.design) get_CDR_start() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_CDR_start_PDB_num() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cdrs_movemap_with_overhang() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) get_cen_scorefxn() (in module pyrosetta.rosetta.protocols.loops) get_cenlist_from_pose() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) get_cenrot_library_by_aa() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary method) get_center_ndx() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) get_center_of_mass() (in module pyrosetta.rosetta.core.pose) get_central_residues() (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) get_central_residues_in_each_of_two_edge_strands() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_central_residues_in_other_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_central_residues_in_this_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_centroid_data() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_centroid_dG() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_centroid_scorefunction() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_centroid_scorefunction_min() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_chain() (in module pyrosetta.rosetta.core.import_pose) get_chain_and_z() (in module pyrosetta.rosetta.protocols.membrane) get_chain_B_resNum() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_chain_break_tolerance() (pyrosetta.rosetta.protocols.LoopRebuild method) get_chain_connections() (in module pyrosetta.rosetta.core.pose.full_model_info) get_chain_for_full_model_resnum() (in module pyrosetta.rosetta.core.pose.full_model_info) get_chain_for_resnum() (in module pyrosetta.rosetta.core.pose.full_model_info) get_chain_from_chain_id() (in module pyrosetta.rosetta.core.pose) get_chain_from_jump_id() (in module pyrosetta.rosetta.core.pose) get_chain_groups() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_chain_id() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) get_chain_id_from_chain() (in module pyrosetta.rosetta.core.pose) get_chain_id_from_jump_id() (in module pyrosetta.rosetta.core.pose) get_chain_id_string() (in module pyrosetta.rosetta.core.conformation.symmetry) get_chain_ids() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) get_chain_ids_from_chain() (in module pyrosetta.rosetta.core.pose) get_chain_ids_from_chains() (in module pyrosetta.rosetta.core.pose) get_chain_residues() (in module pyrosetta.rosetta.core.pose) get_chainbreak_weight() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_chains() (in module pyrosetta.rosetta.core.pose) get_chains_from_cutpoint_open() (in module pyrosetta.rosetta.core.pose.full_model_info) get_chains_from_pdb_info() (in module pyrosetta.rosetta.core.pose.full_model_info) get_chains_full() (in module pyrosetta.rosetta.core.pose.full_model_info) get_cheating_frags() (in module pyrosetta.rosetta.protocols.frags) (pyrosetta.rosetta.protocols.frags.VallData method) get_checkpoints() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) get_chemical_edges() (pyrosetta.rosetta.core.kinematics.FoldTree method) get_chemical_name() (pyrosetta.rosetta.core.chemical.Element method) get_chemical_root_and_anchor_atomnos() (in module pyrosetta.rosetta.core.conformation) get_chemical_symbol() (pyrosetta.rosetta.core.chemical.Element method) get_chi() (pyrosetta.rosetta.core.kinematics.MoveMap method) get_chi_data() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_CHI_energy_function_linkage_type_for_phi_for_residue_in_pose() (in module pyrosetta.rosetta.core.scoring.carbohydrates) get_CHI_energy_function_linkage_type_for_psi_for_residue_in_pose() (in module pyrosetta.rosetta.core.scoring.carbohydrates) get_CHI_energy_function_linkage_type_for_residue_in_pose() (in module pyrosetta.rosetta.core.scoring.carbohydrates) get_children() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) get_children_names() (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) get_chiral_residue_type() (in module pyrosetta.rosetta.protocols.simple_moves.chiral) get_chirality_sign() (in module pyrosetta.rosetta.core.io.pose_from_sfr) get_choice_min_and_max() (in module pyrosetta.rosetta.utility.xsd_util) get_chunk() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) get_clash_and_neighbors() (in module pyrosetta.rosetta.core.pack) get_cloned_saved_pose() (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) get_closest_chain_ending() (in module pyrosetta.rosetta.protocols.denovo_design.components) get_closest_cluster() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher method) get_closest_distance_between_strands() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_closest_non_hoh_contact() (in module pyrosetta.rosetta.protocols.magnesium) get_closest_orbital_axis() (in module pyrosetta.rosetta.core.scoring.magnesium) get_closest_rotamer() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) get_closest_sister() (in module pyrosetta.rosetta.core.io.pose_from_sfr) get_closure_solution() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) get_cluster() (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) get_cluster_data() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) get_cluster_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cluster_for() (pyrosetta.rosetta.protocols.cluster.APCluster method) get_cluster_from_cache_or_ab_info() (in module pyrosetta.rosetta.protocols.antibody.clusters) get_cluster_length() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cluster_name() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cluster_profile_probability_data() (in module pyrosetta.rosetta.protocols.antibody.design) get_co_substrate() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) get_codes_from_NA_consensus_sequence() (in module pyrosetta.rosetta.core.enzymes) get_codes_from_saccharide_consensus_sequence() (in module pyrosetta.rosetta.core.enzymes) get_combine_if_fail_exist() (pyrosetta.rosetta.protocols.LoopRebuild method) get_comment() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.core.io.silent.SilentStruct method) get_complex_energy() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_complexed_sasa() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_component() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) get_component_by_name() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) get_component_lower_bound() (in module pyrosetta.rosetta.core.pose.symmetry) get_component_of_residue() (in module pyrosetta.rosetta.core.pose.symmetry) get_component_upper_bound() (in module pyrosetta.rosetta.core.pose.symmetry) get_computed() (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) get_conformer() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) get_conformer_cen() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) get_connection_domains() (in module pyrosetta.rosetta.core.pose.full_model_info) get_connectivity_annotation_info() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) get_connolly_eggshell() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) get_connolly_eggshell_on_grid() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) get_connolly_surfacePoints() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) get_connolly_surfacePoints_within_grid() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) get_consensus_residues() (pyrosetta.rosetta.core.enzymes.EnzymeManager method) get_consensus_sequence() (pyrosetta.rosetta.core.enzymes.EnzymeManager method) get_consensus_sequence_type() (pyrosetta.rosetta.core.enzymes.EnzymeManager method) get_const_EnzConstraintIO_for_cstfile() (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) get_const_ptr() (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) get_constrain_to_closest() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_constrainable_atoms_map() (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) get_constrained_atom_id() (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) get_constrained_atom_name() (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) get_constraint_for_target_state() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) get_constraint_weight() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) get_constraints_from_file() (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) get_constraints_from_link_records() (in module pyrosetta.rosetta.core.pose) get_constraints_from_pose() (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) get_constraints_only() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) get_contact_resnum_string() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_contact_resnums_string() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) get_contact_selector() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) get_contacts() (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair method) get_continuous_models_from_db() (in module pyrosetta.rosetta.protocols.legacy_sewing) get_coordinates_from_pose() (in module pyrosetta.toolbox.numpy_utils) get_corresponding_residue_in_current() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) get_cos_angle_to_closest_orbital_axis() (in module pyrosetta.rosetta.core.scoring.magnesium) get_cos_theta() (in module pyrosetta.rosetta.core.scoring.magnesium) get_crosslinker_enum() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) get_crosslinker_name() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) get_crossterm_interface_energy() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_crossterm_interface_energy_ratio() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_CSA_data() (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) get_cst_fa_file_option() (in module pyrosetta.rosetta.core.scoring.constraints) get_cst_factory() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) get_cst_file_option() (in module pyrosetta.rosetta.core.scoring.constraints) get_Cstem_foldtree() (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) get_Cter_loop_end() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) get_cterm_insert_flexibility() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) get_cterm_scaffold_flexibility() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) get_cterminal_peptide_bond_reference_frame() (in module pyrosetta.rosetta.core.pose.motif) get_cterminal_peptide_bond_reference_frame_atomids() (in module pyrosetta.rosetta.core.pose.motif) get_cur_ncluster() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) get_current_AntibodyNumberingScheme() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_current_batch() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) get_current_bs_id_and_closest_edge_bs_id_in_different_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_current_CDRDefinition() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_current_confnum() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) get_current_conformer() (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) get_current_for_node() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) get_current_global_sequence() (in module pyrosetta.rosetta.core.pose.full_model_info) get_current_job() (in module pyrosetta.rosetta.protocols.jd2) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) get_current_jobs_starting_pose() (in module pyrosetta.rosetta.protocols.jd2) get_current_output_tag() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) get_current_structure_count() (in module pyrosetta.rosetta.protocols.features) get_current_tag() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) get_cutoff() (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff method) get_cutoff_squared() (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff method) get_cutpoint_closed() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_cutpoint_open_from_chains() (in module pyrosetta.rosetta.core.pose.full_model_info) get_cutpoints_closed() (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) get_cyclization_name_from_type() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) get_cyclization_type_from_name() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) get_D_equivalent() (in module pyrosetta.rosetta.core.chemical) get_d_equivalent() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_data_ndx() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) get_data_score() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) get_database_name() (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) get_database_pq_schema() (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) get_DB_filter_ptr() (in module pyrosetta.rosetta.protocols.features) get_db_session() (in module pyrosetta.rosetta.basic.database) get_DC_data() (pyrosetta.rosetta.core.scoring.DipolarCoupling method) get_DC_data_type() (pyrosetta.rosetta.core.scoring.DC method) get_debug() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) get_debug_rmsd() (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) get_default_task_factory() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) get_definite_terminal_root() (in module pyrosetta.rosetta.core.pose) get_degrees() (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) get_delta_magnetic_anisotropy_deriv() (in module pyrosetta.rosetta.core.scoring.rna.chemical_shift) get_density_map() (in module pyrosetta.rosetta.core.scoring.electron_density_atomwise) get_density_sc_scale_byres() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) get_derivs_from_cycle() (in module pyrosetta.rosetta.core.scoring.power_diagram) get_derivs_from_cycles() (in module pyrosetta.rosetta.core.scoring.power_diagram) get_descriptor() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) get_design() (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) get_design_sequence_motif_syntax() (in module pyrosetta.rosetta.core.sequence) get_desired_loops_exist() (pyrosetta.rosetta.protocols.LoopRebuild method) get_deviation() (in module pyrosetta.rosetta.protocols.loops.loop_closure.ccd) get_DFIRE_potential() (in module pyrosetta.rosetta.core.scoring.methods.dfire) get_discontinuous_models_from_db() (in module pyrosetta.rosetta.protocols.legacy_sewing) get_dist_cutoff() (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) get_dist_cutoff_multiplier() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) get_dist_err() (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) get_distance() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) get_distance_cutoff() (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) get_distance_to_start() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_distinct_sheet_id_from_sheet_table() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_distinct_sw_id_from_sandwich_table() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_distribution() (in module pyrosetta.rosetta.protocols.ligand_docking) get_disulf_partner() (in module pyrosetta.rosetta.core.conformation) get_disulfide_atom_name() (pyrosetta.rosetta.core.chemical.ResidueType method) get_dock_chains() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) get_dock_chains_from_ab_dock_chains() (in module pyrosetta.rosetta.protocols.antibody.design) get_DOF() (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) get_dof_axis_and_end_pos() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) get_dofs_from_energy_map() (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) get_domain() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) get_domain_boundary_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_domain_boundary_suites() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_donor_acceptor_group_from_heavyatom_index() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) get_dot_covered() (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) get_downstream_connections() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) get_downstream_residue_that_this_torsion_moves() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_dsbuilder() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) get_dssp_plus_abego_L_def() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) get_dssp_reduced_IG_as_L_secstruct() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) get_dssp_secstruct() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) get_dssp_unreduced_secstruct() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) get_dun02_aa_parameters() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet method) get_dun10_aa_parameters() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet method) get_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) get_edge_exists() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) get_edge_from_char() (in module pyrosetta.rosetta.core.chemical.rna) get_edge_from_num() (in module pyrosetta.rosetta.core.chemical.rna) get_edge_list_begin() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) get_edge_list_end() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) get_edge_memory_usage() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) get_edge_reweight() (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter method) get_edge_weight() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) get_efficiency() (pyrosetta.rosetta.core.enzymes.EnzymeManager method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) get_eggshell_distance() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) get_electron_affinity() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_electron_configuration() (pyrosetta.rosetta.core.chemical.Element method) get_electronegativity() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_element_type() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_embedded_residue_selector() (in module pyrosetta.rosetta.core.select.residue_selector) get_end_res() (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) get_energy() (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) get_energy_current_state_assignment() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) get_energy_map_from_dofs() (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) get_energy_node() (pyrosetta.rosetta.core.scoring.EnergyGraph method) get_energy_sum_for_vertex_group() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) get_ensured_sites() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) get_environment_dependent_weight() (in module pyrosetta.rosetta.core.scoring.hbonds) get_enzcst_io() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) get_enzdes_observer() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) get_enzyme() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) get_enzyme_family() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) get_epitope_residues() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) get_eps_range() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_epsilon_torsions() (in module pyrosetta.rosetta.core.chemical.rna) get_equiv() (pyrosetta.rosetta.protocols.symmetry.NCSResMapping method) get_euler_angles() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) get_excluded_sites() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) get_exemplar_for() (pyrosetta.rosetta.protocols.cluster.APCluster method) get_extra_cutpoints_from_names() (in module pyrosetta.rosetta.core.import_pose) get_fa_scorefxn() (in module pyrosetta.rosetta.protocols.loops) get_fade_correction() (in module pyrosetta.rosetta.core.scoring.rna) get_favor_native_bonus() (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) get_features_reporter() (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) get_ff() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) get_file_contents() (pyrosetta.rosetta.utility.io.FileContentsMap method) get_file_contents_ref() (pyrosetta.rosetta.utility.io.FileContentsMap method) get_file_option() (in module pyrosetta.rosetta.basic.options) get_file_vector_option() (in module pyrosetta.rosetta.basic.options) get_filename() (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 method) get_filenames() (in module pyrosetta.rosetta.protocols.motifs) get_filter() (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) get_filter_by_phipsi() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) get_filter_names_from_xsd() (in module pyrosetta.rosetta.utility.xsd_util) get_filter_param() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) get_filter_type_by_name() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) get_filter_type_name() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) get_final_fragments() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_final_rot_probs() (in module pyrosetta.rosetta.protocols.make_rot_lib) get_final_rots() (in module pyrosetta.rosetta.protocols.make_rot_lib) get_first_atom() (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData method) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) get_first_index_in_query() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) get_first_index_in_vall() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) get_first_node_ind() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) get_first_protein_residue() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) get_fix_backbone() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_fixed_chains() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_fixed_domain_from_full_model_info_const() (in module pyrosetta.rosetta.core.pose.full_model_info) get_fixed_res() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) get_flags() (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) get_fmax() (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) get_fmin() (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) get_fold_tree() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) get_fold_tree_root() (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) get_FoldTree_AllCDRs() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_FoldTree_AllCDRs_LHDock() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_FoldTree_L_HA() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_FoldTree_LA_H() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_FoldTree_LH_A() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_foldtree_seqsep() (in module pyrosetta.rosetta.protocols.fldsgn.potentials.sspot) get_foldtree_which_partitions() (in module pyrosetta.rosetta.core.kinematics) get_formal_charge() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_fourth_atom() (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) get_fourth_offset() (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) get_fraction() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) get_frag3() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_frag_data() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) get_frag_sizes() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_fragment_library_pointer() (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) get_frags() (in module pyrosetta.rosetta.protocols.frags) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.frags.VallData method) get_frame_ala() (in module pyrosetta.rosetta.core.pose.motif) get_frame_arg() (in module pyrosetta.rosetta.core.pose.motif) get_frame_asn() (in module pyrosetta.rosetta.core.pose.motif) get_frame_asp() (in module pyrosetta.rosetta.core.pose.motif) get_frame_cys() (in module pyrosetta.rosetta.core.pose.motif) get_frame_gln() (in module pyrosetta.rosetta.core.pose.motif) get_frame_glu() (in module pyrosetta.rosetta.core.pose.motif) get_frame_gly() (in module pyrosetta.rosetta.core.pose.motif) get_frame_his() (in module pyrosetta.rosetta.core.pose.motif) get_frame_ile() (in module pyrosetta.rosetta.core.pose.motif) get_frame_leu() (in module pyrosetta.rosetta.core.pose.motif) get_frame_lys() (in module pyrosetta.rosetta.core.pose.motif) get_frame_met() (in module pyrosetta.rosetta.core.pose.motif) get_frame_phe() (in module pyrosetta.rosetta.core.pose.motif) get_frame_pro() (in module pyrosetta.rosetta.core.pose.motif) get_frame_ser() (in module pyrosetta.rosetta.core.pose.motif) get_frame_thr() (in module pyrosetta.rosetta.core.pose.motif) get_frame_trp() (in module pyrosetta.rosetta.core.pose.motif) get_frame_tyr() (in module pyrosetta.rosetta.core.pose.motif) get_frame_val() (in module pyrosetta.rosetta.core.pose.motif) get_from_const_pose() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) get_from_pose() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) get_full_edge_from_num() (in module pyrosetta.rosetta.core.chemical.rna) get_full_intracomponent_and_neighbor_resis() (in module pyrosetta.rosetta.core.pose.symmetry) get_full_intracomponent_and_neighbor_subpose() (in module pyrosetta.rosetta.core.pose.symmetry) get_full_intracomponent_and_neighbor_subs() (in module pyrosetta.rosetta.core.pose.symmetry) get_full_intracomponent_neighbor_resis() (in module pyrosetta.rosetta.core.pose.symmetry) get_full_intracomponent_neighbor_subpose() (in module pyrosetta.rosetta.core.pose.symmetry) get_full_intracomponent_neighbor_subs() (in module pyrosetta.rosetta.core.pose.symmetry) get_full_intracomponent_resis() (in module pyrosetta.rosetta.core.pose.symmetry) get_full_intracomponent_subpose() (in module pyrosetta.rosetta.core.pose.symmetry) get_full_intracomponent_subs() (in module pyrosetta.rosetta.core.pose.symmetry) get_full_LW_orientation_from_num() (in module pyrosetta.rosetta.core.chemical.rna) get_full_orientation_from_num() (in module pyrosetta.rosetta.core.chemical.rna) get_full_side_from_num() (in module pyrosetta.rosetta.core.chemical.rna) get_full_torsions() (in module pyrosetta.rosetta.core.chemical.rna) get_fullatom_scorefunction() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_func() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) get_func_factory() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) get_function() (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData method) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) get_function_names() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) get_G() (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) get_gaussian_deriv() (in module pyrosetta.rosetta.core.scoring.magnesium) get_gaussian_potential_score() (in module pyrosetta.rosetta.core.scoring.magnesium) get_gaussian_score() (in module pyrosetta.rosetta.core.scoring.magnesium) get_gdtmm() (in module pyrosetta.rosetta.protocols.hybridization) get_global_requirement() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory method) get_gly_interface_energy() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_glycan_connecting_protein_branch_point() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_glycan_position_from_resnum() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_glycan_start_points() (in module pyrosetta.rosetta.core.conformation.carbohydrates) get_glycan_tree_set() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) get_glycan_tree_size() (in module pyrosetta.rosetta.core.conformation.carbohydrates) get_glycosidic_bond_residues() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_glycosidic_torsion() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_graft_design_options() (in module pyrosetta.rosetta.protocols.antibody.design) get_grid() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) get_grid_names() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) get_grow_attempts() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) get_H3_kink_type() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_H3_kink_type_name() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_handedness_score_flag() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) get_hardsphere_bump_check() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) get_hash_excluding_chain() (in module pyrosetta.rosetta.core.pose) get_hash_from_chain() (in module pyrosetta.rosetta.core.pose) get_hb_acc_chem_type() (in module pyrosetta.rosetta.core.scoring.hbonds) get_hb_don_chem_type() (in module pyrosetta.rosetta.core.scoring.hbonds) get_hb_e_cutoff() (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) get_hbe_acc_hybrid() (in module pyrosetta.rosetta.core.scoring.hbonds) get_hbond_atom_pairs() (in module pyrosetta.rosetta.protocols.hbnet) get_hbond_energies() (in module pyrosetta.rosetta.core.scoring.hbonds) get_hbond_weight_type() (in module pyrosetta.rosetta.core.scoring.hbonds) get_hbonds() (in module pyrosetta.toolbox) get_helix() (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) get_helix_ends() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) get_highres_scorefxn() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) get_home_dir() (in module pyrosetta.rosetta.utility.file) get_hybrid_orbital_type() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_hydration_stats() (in module pyrosetta.rosetta.protocols.magnesium) get_id() (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) get_ideal_angle_about_contact() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_ideal_angle_about_metal() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_ideal_dihedral_3() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_ideal_dihedral_about_contact() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_ideal_dihedral_about_metal() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_ideal_distance() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_idealize_loop_first() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) get_idx() (in module pyrosetta.rosetta.core.scoring.rna.data) get_idx_for_other_pose() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) get_idx_for_other_pose_with_residue() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) get_idx_for_other_pose_with_residues() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) get_incomplete_connections() (in module pyrosetta.rosetta.protocols.ligand_docking) get_index() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution method) get_indices_of_moving_chunks() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) get_indices_of_voxel_from_coordinates() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) get_init_value() (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) get_input_domain_from_full_model_info_const() (in module pyrosetta.rosetta.core.pose.full_model_info) get_input_pose() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) get_input_res() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) get_input_set_selector() (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) get_input_stub() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) get_instance() (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory method) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager method) (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager method) (pyrosetta.rosetta.core.enzymes.EnzymeManager method) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager method) (pyrosetta.rosetta.core.import_pose.libraries.RNA_LibraryManager method) (pyrosetta.rosetta.core.io.NomenclatureManager method) (pyrosetta.rosetta.core.io.pdb.RecordCollection method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase method) (pyrosetta.rosetta.numeric.model_quality.RmsData method) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory method) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory method) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance method) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory method) get_int() (in module pyrosetta.rosetta.utility.json_spirit) get_int_or_zero() (in module pyrosetta.rosetta.utility.json_spirit) get_integer_option() (in module pyrosetta.rosetta.basic.options) get_integer_vector_option() (in module pyrosetta.rosetta.basic.options) get_interface_delta_hbond_unsat() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_interface_delta_sasa() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_interface_deltas() (in module pyrosetta.rosetta.protocols.ligand_docking) get_interface_dG() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_interface_packstat() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_interface_residues() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) get_interface_set() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_intra_segment_requirement() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory method) get_intracomponent_and_interneighbor_resis() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_and_interneighbor_subpose() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_and_interneighbor_subs() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_and_intraneighbor_resis() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_and_intraneighbor_subpose() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_and_intraneighbor_subs() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_and_neighbor_resis() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_and_neighbor_subpose() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_and_neighbor_subs() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_resis() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_subpose() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_subs() (in module pyrosetta.rosetta.core.pose.symmetry) get_inversion() (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) get_invert_downstream() (pyrosetta.rosetta.core.kinematics.Jump method) get_invert_upstream() (pyrosetta.rosetta.core.kinematics.Jump method) get_ionization_potential() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_is_do_minimize() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_is_dump_cyclic_poses() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_is_dump_peptide_pose() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_is_dump_prepared_pose() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_is_dump_report_file() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_is_report_gzip() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_is_skip_zero_isc() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_iterations() (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) get_iterator_for_tag() (pyrosetta.rosetta.core.io.silent.SilentFileData method) get_jacobian() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) get_jump() (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) get_jump_atom_id() (pyrosetta.rosetta.core.kinematics.AtomTree method) get_jump_atom_ids() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) get_jump_edges() (pyrosetta.rosetta.core.kinematics.FoldTree method) get_jump_id_from_chain() (in module pyrosetta.rosetta.core.pose) get_jump_id_from_chain_id() (in module pyrosetta.rosetta.core.pose) get_jump_ids_from_chain() (in module pyrosetta.rosetta.core.pose) get_jump_ids_from_chain_ids() (in module pyrosetta.rosetta.core.pose) get_jump_name_to_components() (in module pyrosetta.rosetta.core.pose.symmetry) get_jump_name_to_subunits() (in module pyrosetta.rosetta.core.pose.symmetry) get_jump_num() (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) get_jump_selector() (in module pyrosetta.rosetta.core.select.jump_selector) get_jump_that_builds_residue() (pyrosetta.rosetta.core.kinematics.FoldTree method) get_K_cluster_engine() (in module pyrosetta.rosetta.protocols.toolbox) get_km() (in module pyrosetta.rosetta.core.scoring.electron_density) (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) get_known_atoms() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) get_L_equivalent() (in module pyrosetta.rosetta.core.chemical) get_l_equivalent() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_L_move() (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) get_L_prime() (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) get_label() (in module pyrosetta.rosetta.protocols.ss_prediction) get_landmark_resnum() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_largest_chunk_size() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) get_largest_glycan_tree_layer() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_largest_glycan_tree_length() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_largest_glycan_tree_size() (in module pyrosetta.rosetta.core.conformation.carbohydrates) get_last_checkpoint() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) get_last_LoopResult() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) get_last_move_status() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) get_last_protein_residue() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) get_late_factory() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_leap_6dof() (in module pyrosetta.rosetta.protocols.sic_dock) get_leap_lower_stub() (in module pyrosetta.rosetta.protocols.sic_dock) get_leap_upper_stub() (in module pyrosetta.rosetta.protocols.sic_dock) get_legrand_2way_orientation() (in module pyrosetta.rosetta.core.scoring.sasa) get_legrand_atomic_overlap() (in module pyrosetta.rosetta.core.scoring.sasa) get_legrand_orientation() (in module pyrosetta.rosetta.core.scoring.sasa) get_legrand_sasa_angles() (in module pyrosetta.rosetta.core.scoring.sasa) get_legrand_sasa_masks() (in module pyrosetta.rosetta.core.scoring.sasa) get_length() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) get_library_by_aa() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) get_ligand_atom_name() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_ligand_grid_scores() (in module pyrosetta.rosetta.protocols.ligand_docking) get_ligand_id() (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) get_ligand_jump_id() (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_ligand_resnum() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_ligand_resnum_string() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_ligand_RMSDs() (in module pyrosetta.rosetta.protocols.ligand_docking) get_ligand_selector() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_ligand_seqpos() (in module pyrosetta.rosetta.protocols.ligand_docking) get_ligand_torsion_constraints() (in module pyrosetta.rosetta.protocols.ligand_docking) get_ligand_travel() (in module pyrosetta.rosetta.protocols.ligand_docking) get_ligand_travel_ensemble_best() (in module pyrosetta.rosetta.protocols.ligand_docking) get_ligand_weight() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_LigandMotifLibrary_user() (in module pyrosetta.rosetta.protocols.motifs) get_light_chain_type() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_light_chain_type_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_lines_from_file_data() (in module pyrosetta.rosetta.utility.io) get_link_record() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) get_linkage_position() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_linkage_position_of_saccharide_residue() (in module pyrosetta.rosetta.core.conformation.carbohydrates) get_linker_index_asymmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) get_linker_indices_symmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) get_list_of_custom_variants() (pyrosetta.rosetta.core.chemical.ResidueProperties method) get_list_of_custom_variants_by_reference() (pyrosetta.rosetta.core.chemical.ResidueProperties method) get_list_of_properties() (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) get_list_of_variant_enums() (pyrosetta.rosetta.core.chemical.ResidueProperties method) get_list_of_variants() (pyrosetta.rosetta.core.chemical.ResidueProperties method) get_lj_hbond_dis() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) get_lj_hbond_hdis() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) get_lj_hbond_OH_donor_dis() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) get_loaded_job_indices() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) get_localstrandpair_penalty() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) get_logger() (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) get_loop() (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) get_loop_atom() (in module pyrosetta.rosetta.core.scoring.loop_graph) get_loop_close_potential() (in module pyrosetta.rosetta.core.scoring.loop_graph) get_loop_combine_rate() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) get_loop_file() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_loop_file_reader() (pyrosetta.rosetta.protocols.loops.Loops method) get_loop_info() (in module pyrosetta.rosetta.protocols.mpi_refinement) get_loop_info_full() (in module pyrosetta.rosetta.protocols.mpi_refinement) get_loop_sequence() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) get_loop_size() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) get_loops() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) get_lower_cutpoint_partner_for_upper() (in module pyrosetta.rosetta.core.scoring.methods) get_LW_orientation() (in module pyrosetta.rosetta.core.pose.rna) get_LW_orientation_from_char() (in module pyrosetta.rosetta.core.chemical.rna) get_LW_orientation_from_num() (in module pyrosetta.rosetta.core.chemical.rna) get_main_group() (pyrosetta.rosetta.core.chemical.Element method) get_mainchain_child() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) get_mainchain_children() (in module pyrosetta.rosetta.core.pose.carbohydrates) get_manager() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) get_map() (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap method) get_mArray() (in module pyrosetta.rosetta.utility.json_spirit) get_masks() (in module pyrosetta.rosetta.core.scoring) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) get_matching_landmark() (in module pyrosetta.rosetta.protocols.antibody) get_max0() (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) get_max_angle_dev() (pyrosetta.rosetta.protocols.membrane.FlipMover method) get_max_attempts() (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) get_max_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) get_max_centroid_to_atom_distance() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body) get_max_dist_ndx() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) get_max_distance() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) get_max_dslf_energy() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) get_max_dslf_pot() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) get_max_nstruct() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) get_max_rms() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) get_max_sheet_id() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_max_strand_dist_cutoff() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) get_maxE_contribution_to_pi_system() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_maximum_scores() (in module pyrosetta.rosetta.core.sequence) get_mc() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) get_membrane_depth_dependent_weight() (in module pyrosetta.rosetta.core.scoring.hbonds) get_metal_binding_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) get_metal_resnums_string() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) get_metal_selector() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) get_metals_angle_constraint_multiplier() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) get_metals_detection_LJ_multiplier() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) get_metals_distance_constraint_multiplier() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) get_metric_from_datamap_and_subtags() (in module pyrosetta.rosetta.core.simple_metrics) get_metric_names() (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.TotalEnergyMetric method) get_metrics_from_datamap_and_subtags() (in module pyrosetta.rosetta.core.simple_metrics) get_mg_ligands() (in module pyrosetta.rosetta.protocols.magnesium) get_mg_res() (in module pyrosetta.rosetta.protocols.magnesium) get_mg_rsd() (in module pyrosetta.rosetta.protocols.magnesium) get_mg_scorefxn() (in module pyrosetta.rosetta.protocols.magnesium) get_mg_water_pairs() (in module pyrosetta.rosetta.protocols.magnesium) get_middle_residue() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) get_middle_ss() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) get_min0() (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) get_min_allowed_score() (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) get_min_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) get_min_options() (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) get_min_rms() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) get_min_type() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) get_minimization_node() (pyrosetta.rosetta.core.scoring.MinimizationGraph method) get_minimize_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_minval_binwidth() (in module pyrosetta.rosetta.core.scoring.loop_graph.evaluator) get_mirrored_type() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_missing_template_other_res() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) get_missing_template_res() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) get_mObject() (in module pyrosetta.rosetta.utility.json_spirit) get_model_node() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) get_model_segments() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) get_modeler_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) get_module_names_from_xsd() (in module pyrosetta.rosetta.utility.xsd_util) get_module_type_as_it_appears_in_xsd() (in module pyrosetta.rosetta.utility.xsd_util) get_most_recent_total_score() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) get_motif_atom_mask() (in module pyrosetta.rosetta.core.scoring.motif) get_motif_build_position_defs_user() (in module pyrosetta.rosetta.protocols.motifs) get_motif_build_positions_user() (in module pyrosetta.rosetta.protocols.motifs) get_motif_length() (in module pyrosetta.rosetta.core.sequence) get_MotifLibrary_user() (in module pyrosetta.rosetta.protocols.motifs) get_move_elements_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) get_move_elements_from_full_model_info_const() (in module pyrosetta.rosetta.core.pose.full_model_info) get_move_type_string() (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo) get_movemap() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) get_movemap_factory() (in module pyrosetta.rosetta.core.select.movemap) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) get_MoveMap_for_AllCDRsSideChains_and_H3backbone() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_MoveMap_for_Loops() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_MoveMap_for_LoopsandDock() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_movemap_from_task() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) get_movement() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) get_mover() (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) get_mover_cycles() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) get_mover_names_from_xsd() (in module pyrosetta.rosetta.utility.xsd_util) get_moving_res() (in module pyrosetta.rosetta.protocols.rna.denovo) get_moving_res_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) get_moving_res_from_full_model_info_const() (in module pyrosetta.rosetta.core.pose.full_model_info) get_moving_res_including_domain_boundaries() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_multi_residue_ligand_RMSDs() (in module pyrosetta.rosetta.protocols.ligand_docking) get_multichain_constructor() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_n_alignments() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) get_n_bb() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_N_C_stems_foldtree() (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) get_n_candidates() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_n_centroids() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_n_chi() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_n_co_substrates() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) get_n_cyd_seqpos() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) get_n_frags() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_n_glycosidic_torsions_in_res() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_n_partners() (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) get_n_reactive_sites() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) get_n_residue_groups() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) get_n_residue_types() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) get_n_rotamers_for_residue_group() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) get_n_rotamers_for_residue_type() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) get_NACCESS_SASA_radii() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData method) get_NACCESS_SASA_radii_with_expanded_polars() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData method) get_name() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AROMATIC method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.CHARGED method) (pyrosetta.rosetta.core.pack.task.EMPTY method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NC method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.PIKRNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PROPERTY method) (pyrosetta.rosetta.core.pack.task.RESET method) (pyrosetta.rosetta.core.pack.task.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method)

get_name_individual_mover() (pyrosetta.rosetta.protocols.moves.RandomMover method) get_native_pose() (in module pyrosetta.rosetta.protocols.constraint_generator) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) get_native_sequence() (in module pyrosetta.rosetta.protocols.antibody.design) get_natom() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) get_natoms() (pyrosetta.rosetta.core.scoring.PQR method) get_nbrs() (in module pyrosetta.rosetta.core.scoring.motif) get_ndata() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) get_ndx_list() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) get_near_interface_residues() (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) get_neighbor_distance() (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) get_neighbor_residues() (in module pyrosetta.rosetta.core.select) get_neighbor_resis() (in module pyrosetta.rosetta.core.pose.symmetry) get_neighbor_subpose() (in module pyrosetta.rosetta.core.pose.symmetry) get_neighbor_subs() (in module pyrosetta.rosetta.core.pose.symmetry) get_net_sim() (pyrosetta.rosetta.protocols.cluster.APCluster method) get_new_job_id() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) get_next_reference_node() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) get_next_starting_res_for_connecting_strands() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_nmoves() (pyrosetta.rosetta.protocols.moves.RepeatMover method) get_nNumber_hybrid_lone_pairs() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_no_design_cys() (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) get_no_frags() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_node() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) get_node_index() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) get_node_indices_from_model_id() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) get_node_option() (in module pyrosetta.rosetta.utility.xsd_util) get_non_bb_clashing_rotamers() (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) get_non_NU_TorsionID_from_AtomIDs() (in module pyrosetta.rosetta.core.conformation.carbohydrates) get_nonjump_atom() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) get_nonpivot_torsion_sampling() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) get_nonzero_weighted_scoretypes() (pyrosetta.rosetta.core.scoring.ScoreFunction method) get_normal_to_plane() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_npdhb_simple_node() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) get_nres_asu() (in module pyrosetta.rosetta.protocols.cryst) get_nres_asymmetric_unit() (in module pyrosetta.rosetta.core.pose.symmetry) get_Nstem_foldtree() (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) get_nterm_insert_flexibility() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) get_nterm_scaffold_flexibility() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) get_nterminal_peptide_bond_reference_frame() (in module pyrosetta.rosetta.core.pose.motif) get_nterminal_peptide_bond_reference_frame_atomids() (in module pyrosetta.rosetta.core.pose.motif) get_nu() (pyrosetta.rosetta.core.kinematics.MoveMap method) get_num_aatypes() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) get_num_atoms() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) get_num_bytes() (in module pyrosetta.rosetta.core.scoring) get_num_covered() (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) get_num_covered_total() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) get_num_digits() (in module pyrosetta.rosetta.utility) get_num_edges() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) get_num_edges_for_res() (in module pyrosetta.rosetta.protocols.hbnet) get_num_edges_to_larger_indexed_nodes() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) get_num_edges_to_smaller_indexed_nodes() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) get_num_exemplars() (pyrosetta.rosetta.protocols.cluster.APCluster method) get_num_interface_residues() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_num_nodes() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) get_num_of_distinct_sheet_id() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_num_of_sheets_that_surround_this_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_num_protein_sc_sc_hbonds() (in module pyrosetta.rosetta.protocols.hbnet) get_num_residues_nonvirt() (in module pyrosetta.rosetta.protocols.hybridization) get_num_residues_prot() (in module pyrosetta.rosetta.protocols.hybridization) get_num_rpe_calculations_count() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) get_num_states_for_node() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) get_num_strands_in_this_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_num_total_states() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) get_num_uncovered() (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) get_num_unrecognized_atoms() (pyrosetta.rosetta.core.pose.PDBInfo method) get_num_unrecognized_res() (pyrosetta.rosetta.core.pose.PDBInfo method) get_number_base_pairs() (in module pyrosetta.rosetta.core.pose.rna) get_number_base_stacks() (in module pyrosetta.rosetta.core.pose.rna) get_number_bonds() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_number_dihedrals() (in module pyrosetta.rosetta.protocols.ncbb) get_number_electrons_in_bonds() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_number_electrons_in_p_orbitals() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_number_hybrid_bonds() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_number_hybrid_orbitals() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_number_missing_residues_and_connections() (in module pyrosetta.rosetta.core.pose.full_model_info) get_number_native_base_pairs() (in module pyrosetta.rosetta.core.pose.rna) get_number_pi_orbitals() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_number_sigma_orbitals() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_number_unhybridized_lone_pairs() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_number_unhybridized_sigma_orbitals() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_numeric_property() (pyrosetta.rosetta.core.chemical.ResidueType method) get_octahedral_uniform_rotation_sampler() (in module pyrosetta.rosetta.protocols.magnesium) get_offset() (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData method) get_omega_preference_for_residue_in_pose() (in module pyrosetta.rosetta.core.scoring.carbohydrates) get_omg_range() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_one_body_energy_for_node_state() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) get_one_patch() (pyrosetta.rosetta.core.chemical.Metapatch method) get_one_template_pose() (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) get_op2_op1_sign() (in module pyrosetta.rosetta.core.pose.rna) get_open_mode() (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) get_optimize1() (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) get_optimize2() (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) get_optimize_cyclic_threshold() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_option_type_from_name() (in module pyrosetta.rosetta.utility.xsd_util) get_options() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) get_orbital_E_neg_pos() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_orientation() (in module pyrosetta.rosetta.core.scoring) (in module pyrosetta.rosetta.core.scoring.packstat.old) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) get_orientation_from_char() (in module pyrosetta.rosetta.core.chemical.rna) get_orientation_from_num() (in module pyrosetta.rosetta.core.chemical.rna) get_original_pose_rsd() (in module pyrosetta.rosetta.protocols.generalized_kinematic_closure) get_original_residue() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) get_original_residue_set() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) get_other_ind() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) get_other_node() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) get_other_poses() (in module pyrosetta.rosetta.core.import_pose) get_out() (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) get_out_tag() (in module pyrosetta.rosetta.protocols.vip) get_outfile_name_with_tag() (in module pyrosetta.rosetta.core.io.silent) get_outgoing_edges() (pyrosetta.rosetta.core.kinematics.FoldTree method) get_output_filename() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) get_output_tag() (in module pyrosetta.rosetta.protocols.jobdist) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) get_overlap() (in module pyrosetta.rosetta.core.scoring) (in module pyrosetta.rosetta.core.scoring.packstat.old) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) get_pack_input() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_pack_neighbors() (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) get_packer() (in module pyrosetta.rosetta.protocols.stepwise.modeler.packer) get_packer_task() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_PackingAngleResidues() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_pair() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) get_pairing_geometry() (in module pyrosetta.rosetta.core.scoring.dssp) (in module pyrosetta.rosetta.protocols.jumping) get_parallel_weight() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) get_parameters() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) get_parametric_info() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) get_parent() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_parent_remark() (pyrosetta.rosetta.core.io.silent.SilentStruct method) get_parent_remark_from_line() (pyrosetta.rosetta.core.io.silent.SilentStruct method) get_parent_residue() (pyrosetta.rosetta.core.kinematics.FoldTree method) get_partition_definition() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_partition_definition_by_jump() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_partition_definition_floating_base() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) get_partner() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) get_partner_residue_start_stop() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_partners() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) get_patch_names() (in module pyrosetta.rosetta.core.chemical) get_path_option() (in module pyrosetta.rosetta.basic.options) get_path_vector_option() (in module pyrosetta.rosetta.basic.options) get_PCS_data_input_reference() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 method) get_PCS_data_line_all_reference() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 method) get_PCS_experimental() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) get_PCS_tolerance() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) get_PcsInputFile_all() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter method) get_PcsInputLine_all() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile method) get_pdb2pose_numbering_as_stdmap() (in module pyrosetta.rosetta.core.pose) get_pdb_and_cleanup() (in module pyrosetta.rosetta.core.import_pose) get_pdb_code_from_pose_tag() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) get_pdb_id() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) get_pdb_numbering_from_single_string() (in module pyrosetta.rosetta.protocols.antibody.design) get_pdb_numbering_from_strings() (in module pyrosetta.rosetta.protocols.antibody.design) get_pdb_remark() (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) get_pdb_with_full_model_info() (in module pyrosetta.rosetta.core.import_pose) get_pep_lengths() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_peptide() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) get_peptide_bond_reference_frame() (in module pyrosetta.rosetta.core.pose.motif) get_peptide_bond_reference_frame_atomids() (in module pyrosetta.rosetta.core.pose.motif) get_peptide_chain() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) get_per_residue_energy() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_per_residue_score() (in module pyrosetta.rosetta.protocols.nonlocal) get_per_residue_scores() (in module pyrosetta.rosetta.protocols.relax) get_percentile_bounds() (in module pyrosetta.rosetta.numeric.kdtree) get_period() (pyrosetta.rosetta.core.chemical.Element method) get_perturb_CCD_off() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) get_perturb_cycles() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) get_perturb_KIC_off() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) get_perturb_show() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) get_perturb_temp() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) get_perturber_effect() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) get_perturber_effect_from_name() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) get_perturber_effect_name() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) get_perturber_names() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) get_phosphate_atom_and_neighbor_list() (in module pyrosetta.rosetta.core.pose.rna) get_phosphate_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) get_pi_electron_contribution_type() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_picked_positions() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_pivot_picker() (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) get_pivot_residues_from_movemap() (in module pyrosetta.rosetta.protocols.backrub) get_pleating() (in module pyrosetta.rosetta.core.scoring.dssp) (in module pyrosetta.rosetta.protocols.jumping) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) get_pocket_distance() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) get_PolycubicSpline_F() (in module pyrosetta.rosetta.numeric.interpolation.spline) get_PolycubicSpline_gradient() (in module pyrosetta.rosetta.numeric.interpolation.spline) get_polymer_residue_direction() (pyrosetta.rosetta.core.kinematics.FoldTree method) get_polymer_type() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_pool() (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) get_pool_bins() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) get_pool_name() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) get_pose() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.Job method) get_pose_build_resids() (pyrosetta.rosetta.protocols.match.Matcher method) get_pose_cis_trans_conformation() (in module pyrosetta.rosetta.protocols.antibody.clusters) get_pose_data() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) get_pose_from_claimer() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) get_pose_list() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) get_poses() (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) get_possible_O3prime_C5prime_distance_range() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) get_possible_reference_res_list_from_pose_without_fold_tree() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) get_prediction_name() (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) get_prefix() (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) get_pretend_phi_explicit() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) get_pretend_psi_explicit() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) get_primary_graft_mover() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) get_principal_quantum_number() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) get_priority() (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) get_prob() (in module pyrosetta.rosetta.protocols.ss_prediction) get_profile() (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) get_property() (pyrosetta.rosetta.core.chemical.Element method) get_property_from_string() (pyrosetta.rosetta.core.chemical.ResidueProperties method) get_property_name() (pyrosetta.rosetta.core.chemical.Element method) get_protocol_and_batch_id() (in module pyrosetta.rosetta.protocols.features) get_proxy_by_priority() (pyrosetta.rosetta.basic.TracerImpl method) get_pseudobonds_to_residue() (pyrosetta.rosetta.core.conformation.Residue method) get_ptask() (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) get_ptr() (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) get_pymol_chain() (in module pyrosetta.rosetta.basic) get_pymol_chain_index_1() (in module pyrosetta.rosetta.basic) get_pymol_num_unique_ids() (in module pyrosetta.rosetta.basic) get_pymol_observer() (in module pyrosetta.rosetta.protocols.moves) get_pymol_sel_hbond_unsat() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_pymol_sel_interface() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_pymol_sel_packing() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_python_string() (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) get_qt_mapping_general() (in module pyrosetta.rosetta.protocols.comparative_modeling) get_query_middle_res_id() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) get_query_phi_prediction() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_query_phi_prediction_conf() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_query_pos_i() (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair method) get_query_pos_j() (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair method) get_query_psi_prediction() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_query_psi_prediction_conf() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_query_residue_depth() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_query_sa_prediction() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_query_seq() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_query_seq_string() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_query_size() (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) get_query_ss() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_query_ss_string() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_question_mark_string() (in module pyrosetta.rosetta.protocols.features) get_quota_score() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) get_radial_disp_diffs() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) get_radial_disps() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) get_radii() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) get_radius() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) get_radius_of_gyration() (in module pyrosetta.rosetta.protocols.ligand_docking) get_rama_check() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) get_rama_prepro_mainchain_torsion_potential_name() (pyrosetta.rosetta.core.chemical.ResidueType method) get_rama_prepro_map_file_name() (pyrosetta.rosetta.core.chemical.ResidueType method) get_random_angle() (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) get_random_backbone_segments() (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) get_random_base_pair_jump() (pyrosetta.rosetta.core.import_pose.libraries.RNA_JumpLibrary method) get_random_beta_sheet_jump() (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) get_random_loop_flag() (pyrosetta.rosetta.protocols.LoopRebuild method) get_random_node() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) get_random_node_with_edges() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) get_random_order() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) get_random_point_on_ellipsoid() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_random_tmh_jump() (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) get_randomize_resnum() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_raw_const_ptr() (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) get_raw_ptr() (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) get_rb_atr_and_rep_scores() (in module pyrosetta.rosetta.protocols.ligand_docking) get_rb_center() (pyrosetta.rosetta.core.kinematics.Jump method) get_rb_delta() (pyrosetta.rosetta.core.kinematics.Jump method) get_rb_number() (in module pyrosetta.rosetta.core.id) get_rb_type() (in module pyrosetta.rosetta.core.id) get_RDC_data() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) get_RDC_data_type() (pyrosetta.rosetta.core.scoring.RDC method) get_rdf_function() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) get_reactive_atom() (pyrosetta.rosetta.core.enzymes.EnzymeManager method) get_reactive_residue_consensus_sequence_position() (pyrosetta.rosetta.core.enzymes.EnzymeManager method) get_reactive_site_atom_name() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) get_reactive_site_sequence_position() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) get_ready_for_sew_packing() (in module pyrosetta.rosetta.protocols.hydrate) get_real() (in module pyrosetta.rosetta.utility.json_spirit) get_Real_MathNTensor_dimension_size() (in module pyrosetta.rosetta.numeric) get_real_option() (in module pyrosetta.rosetta.basic.options) get_real_or_zero() (in module pyrosetta.rosetta.utility.json_spirit) get_real_vector_option() (in module pyrosetta.rosetta.basic.options) get_recces_turner_sampler() (in module pyrosetta.rosetta.protocols.recces.sampler) get_recognized_cdr_definitions() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) get_recognized_cluster_definitions() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) get_recognized_numbering_schemes() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) get_ref_tags() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) get_reference_atoms() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_reference_atoms_for_1st_omega() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_reference_atoms_for_2nd_omega() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_reference_atoms_for_phi() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_reference_atoms_for_psi() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_reference_energies_from_dofs() (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) get_reference_energy() (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) get_reference_pose() (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) get_reference_res_for_each_virtual_sugar_based_on_fold_tree() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) get_reference_res_for_each_virtual_sugar_without_fold_tree() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) get_reference_res_for_virtual_sugar_based_on_fold_tree() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) get_region_of_residue() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_register() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) get_rel_hphobic_sasa_by_charge() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_relevant_residues_mode() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) get_remark_line() (in module pyrosetta.rosetta.protocols.denovo_design) get_remove_hydrogens() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) get_repack_period() (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) get_report_as() (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) get_report_format() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_representative_type_aa() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_representative_type_base_name() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_representative_type_name1() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_representative_type_name3() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_res_energy() (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) get_res_list_const() (in module pyrosetta.rosetta.core.pose.full_model_info) get_res_list_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) get_res_list_from_full_model_info_const() (in module pyrosetta.rosetta.core.pose.full_model_info) get_res_num_from_pdb_info() (in module pyrosetta.rosetta.core.pose.full_model_info) get_res_res_elecE() (pyrosetta.rosetta.core.scoring.GenBornPotential method) get_res_res_score() (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) get_res_res_vdw() (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) get_res_type_set() (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) get_resfile_1() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_resfile_2() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_resfile_commands() (in module pyrosetta.rosetta.core.pack.task) get_resid() (in module pyrosetta.rosetta.protocols.denovo_design) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.moves.ResId method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) get_residue() (in module pyrosetta.rosetta.core.pose.full_model_info) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) get_residue_base_state() (in module pyrosetta.rosetta.core.chemical.rna) (in module pyrosetta.rosetta.core.pose.rna) get_residue_depth() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) get_residue_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) get_residue_from_name() (in module pyrosetta.rosetta.core.conformation) get_residue_from_name1() (in module pyrosetta.rosetta.core.conformation) get_residue_group_begin() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) get_residue_group_index_for_rotamer() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) get_residue_hsasa() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_residue_hsasa_bb() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_residue_hsasa_sc() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_residue_level_task_operation_names_from_xsd() (in module pyrosetta.rosetta.utility.xsd_util) get_residue_mapping_from_selectors() (in module pyrosetta.rosetta.core.select.residue_selector) get_residue_mask() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) get_residue_num() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) get_residue_pair_rt6() (in module pyrosetta.rosetta.core.scoring.motif) get_residue_pair_xform() (in module pyrosetta.rosetta.core.scoring.motif) get_residue_path_distances() (in module pyrosetta.rosetta.core.chemical) get_residue_pucker_state() (in module pyrosetta.rosetta.core.chemical.rna) (in module pyrosetta.rosetta.core.pose.rna) get_residue_residue_h2o_hbonds_1way() (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) get_residue_sasa() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_residue_sasa_bb() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_residue_sasa_sc() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_residue_selector() (in module pyrosetta.rosetta.core.select.residue_selector) (in module pyrosetta.rosetta.protocols.denovo_design) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) get_residue_selector_from_subset() (in module pyrosetta.rosetta.core.select) get_residue_selector_names_from_xsd() (in module pyrosetta.rosetta.utility.xsd_util) get_residue_set_from_subset() (in module pyrosetta.rosetta.core.select) get_residue_type_begin() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) get_residue_type_index_for_rotamer() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) get_residue_type_set() (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) get_residue_type_with_variant_added() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_residue_type_with_variant_removed() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_residue_weight() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) get_residue_weight_by_ss() (in module pyrosetta.rosetta.core.scoring.methods) get_residues() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation method) get_residues_from_chains() (in module pyrosetta.rosetta.core.pose) get_residues_from_movemap_bb_any_torsion() (in module pyrosetta.rosetta.core.kinematics) get_residues_from_movemap_bb_or_chi() (in module pyrosetta.rosetta.core.kinematics) get_residues_from_movemap_with_id() (in module pyrosetta.rosetta.core.kinematics) get_residues_from_subset() (in module pyrosetta.rosetta.core.select) get_residues_to_rebuild() (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) get_residues_within_dist_of_RNA() (in module pyrosetta.rosetta.protocols.rna.denovo) get_resis() (in module pyrosetta.rosetta.core.pose.symmetry) get_reslabels() (pyrosetta.rosetta.core.pose.PDBInfo method) get_resnum() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_resnum_and_chain() (in module pyrosetta.rosetta.utility) get_resnum_and_chain_and_segid() (in module pyrosetta.rosetta.utility) get_resnum_and_chain_from_one_tag() (in module pyrosetta.rosetta.utility) get_resnum_and_segid() (in module pyrosetta.rosetta.utility) get_resnum_and_segid_from_one_tag() (in module pyrosetta.rosetta.utility) get_resnum_from_cstid() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) get_resnum_from_cstid_list() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) get_resnum_from_glycan_position() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_resnum_from_pdb_numbering() (in module pyrosetta.rosetta.protocols.antibody.design) get_resnum_from_single_string() (in module pyrosetta.rosetta.protocols.antibody.design) get_resnum_from_single_string_w_landmark() (in module pyrosetta.rosetta.protocols.antibody.design) get_resnum_from_strings() (in module pyrosetta.rosetta.protocols.antibody.design) get_resnum_list() (in module pyrosetta.rosetta.core.pose) get_resnum_list_ordered() (in module pyrosetta.rosetta.core.pose) get_resnum_selector() (in module pyrosetta.rosetta.core.pose) get_resnum_string() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) get_resnum_to_subunit_component() (in module pyrosetta.rosetta.core.pose.symmetry) get_resnumber_from_reference_pose() (in module pyrosetta.rosetta.core.pose) get_resnums_for_chain() (in module pyrosetta.rosetta.core.pose) get_resnums_for_chain_id() (in module pyrosetta.rosetta.core.pose) get_resnums_from_glycan_positions() (in module pyrosetta.rosetta.core.pose.carbohydrates) get_resnums_from_strings_with_ranges() (in module pyrosetta.rosetta.protocols.antibody.design) get_resnums_in_leaf() (in module pyrosetta.rosetta.core.pose.carbohydrates) get_resnums_in_leaf_on_the_fly() (in module pyrosetta.rosetta.core.pose.carbohydrates) get_restrict_partners_to_chains() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_restrict_receptors_to_chains() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_restype_for_pose() (in module pyrosetta.rosetta.core.pose) get_result() (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) get_rg() (in module pyrosetta.rosetta.protocols.sic_dock) get_rigid_body_confs() (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) get_rigid_body_jumps() (in module pyrosetta.rosetta.core.pose.rna) get_rigid_body_mover() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_ring_current_deriv() (in module pyrosetta.rosetta.core.scoring.rna.chemical_shift) get_rmsd() (in module pyrosetta.rosetta.protocols.loophash) (in module pyrosetta.rosetta.protocols.stepwise.modeler.align) get_rmsd_tolerance() (pyrosetta.rosetta.protocols.LoopRebuild method) get_rmsd_type_name_map() (in module pyrosetta.rosetta.protocols.analysis.simple_metrics) get_rmsd_type_names() (in module pyrosetta.rosetta.protocols.analysis.simple_metrics) get_rna_base_centroid() (in module pyrosetta.rosetta.core.chemical.rna) get_rna_base_coordinate_system() (in module pyrosetta.rosetta.core.chemical.rna) get_rna_base_coordinate_system_from_CS_params() (in module pyrosetta.rosetta.core.scoring.rna.chemical_shift) get_rna_base_coordinate_system_stub() (in module pyrosetta.rosetta.core.chemical.rna) get_RNA_CS_residue_parameters() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters method) get_rna_data_info() (in module pyrosetta.rosetta.core.io.rna) get_rna_hires_scorefxn() (in module pyrosetta.rosetta.protocols.rna.denovo) get_rna_motif_score() (in module pyrosetta.rosetta.core.scoring.rna) get_rna_motifs() (in module pyrosetta.rosetta.core.scoring.rna) get_rna_secstruct_legacy() (in module pyrosetta.rosetta.core.pose.rna.secstruct_legacy) get_rna_secstruct_legacy_from_const_pose() (in module pyrosetta.rosetta.core.pose.rna.secstruct_legacy) get_rna_stack_score() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) get_rnp_docking_fold_tree() (in module pyrosetta.rosetta.protocols.rna.denovo) get_root() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) get_root_atomno() (in module pyrosetta.rosetta.core.conformation) get_root_residue_root_atomno() (in module pyrosetta.rosetta.core.conformation) get_ROSETTA_SASA_radii() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData method) get_rot_ind() (pyrosetta.rosetta.protocols.mean_field.ResHashMap method) get_rot_mag() (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) get_rot_magnitude() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) get_rotamer_angle_diffs() (in module pyrosetta.rosetta.core.pack) get_rotamer_bounding_box() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) get_rotamer_recovery() (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) get_rotamer_recovery_comparer() (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) get_rotamer_recovery_protocol() (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) get_rotamer_recovery_reporter() (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) get_rotamer_samples() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) get_rotamers_born_radii() (pyrosetta.rosetta.core.scoring.FACTSPotential method) (pyrosetta.rosetta.core.scoring.GenBornPotential method) get_rotamers_vdw_info() (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) get_rotation() (pyrosetta.rosetta.core.kinematics.Jump method) get_rotation_magnitude() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_rotation_matrix() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_rotation_std_dev() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_rsd_type_from_aa() (in module pyrosetta.rosetta.core.pose) get_rsd_type_name3() (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) get_rt_from_residue_pair() (in module pyrosetta.rosetta.core.conformation) get_rt_over_leap() (in module pyrosetta.rosetta.protocols.loophash) get_rt_over_leap_fast() (in module pyrosetta.rosetta.protocols.loophash) get_rt_over_leap_without_foldtree_bs() (in module pyrosetta.rosetta.protocols.loophash) get_run_time() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) get_safe_max_dis2() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) get_sample_index() (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) get_sample_nonpivot_torsions() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) get_sample_res_for_pose() (in module pyrosetta.rosetta.core.pose.full_model_info) get_sampler_options() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) get_sampling_data() (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction method) get_sasa() (in module pyrosetta.rosetta.core.scoring.motif) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) get_sasa_dot_locations() (in module pyrosetta.rosetta.core.scoring.packstat) get_sasa_from_cycles() (in module pyrosetta.rosetta.core.scoring.power_diagram) get_sasa_method_from_string() (in module pyrosetta.rosetta.core.scoring.sasa) get_sasa_radii_parameter_name() (in module pyrosetta.rosetta.core.scoring.sasa) get_sasa_radii_set_from_string() (in module pyrosetta.rosetta.core.scoring.sasa) get_sc_bb_sasa() (in module pyrosetta.rosetta.core.scoring.sasa) get_sc_bb_sasa_per_res() (in module pyrosetta.rosetta.core.scoring.sasa) get_scdepth_avrg() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) get_scdepth_fvar() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) get_scdepth_sdev() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) get_score() (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) get_score_against_internal_contacts() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_score_components() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) get_score_for_struct_id_and_score_term_from_job_data() (in module pyrosetta.rosetta.protocols.features) get_score_for_struct_id_and_score_term_from_score_data() (in module pyrosetta.rosetta.protocols.features) get_score_function() (in module pyrosetta.rosetta.core.scoring) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) get_score_function_attributes() (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) get_score_function_legacy() (in module pyrosetta.rosetta.core.scoring) get_score_function_name() (in module pyrosetta.rosetta.core.scoring) get_score_functionName() (in module pyrosetta.rosetta.core.scoring) get_score_fxn() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_score_line_string() (in module pyrosetta.rosetta.core.pose) get_score_manager() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_score_map() (in module pyrosetta.rosetta.protocols.jobdist) get_score_name() (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) get_score_normalization_function() (in module pyrosetta.rosetta.protocols.qsar.scoring_grid) get_score_result() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) get_score_type_id_from_score_term() (in module pyrosetta.rosetta.protocols.features) get_scorefunction() (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) get_scorefxn() (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) get_scorefxn_deriver() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_scorefxn_info() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) get_scoretypes() (in module pyrosetta.rosetta.protocols.recces) get_SDE_score() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) get_second_atom() (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData method) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) get_second_atom_from_connection() (in module pyrosetta.rosetta.core.conformation) get_second_node_ind() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) get_second_offset() (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) get_second_substrates_or_byproducts() (pyrosetta.rosetta.core.enzymes.EnzymeManager method) get_secondary_graft_mover() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) get_secondary_prediction() (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) get_secstruct() (in module pyrosetta.rosetta.protocols.membrane) (in module pyrosetta.toolbox) (pyrosetta.rosetta.core.pose.rna.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) get_seed() (pyrosetta.rosetta.numeric.random.RandomGenerator method) get_segids_from_pdb_info() (in module pyrosetta.rosetta.core.pose.full_model_info) get_segment_id() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_selected_mover() (pyrosetta.rosetta.protocols.moves.SwitchMover method) get_selector_type() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) get_selector_type_by_name() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) get_selector_type_name() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) get_self_ptr() (pyrosetta.rosetta.basic.datacache.CacheableData method) (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringIntegerMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphContainer method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) (pyrosetta.rosetta.core.scoring.DipolarCoupling method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.NCSResMapping method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) get_self_weak_ptr() (pyrosetta.rosetta.basic.datacache.CacheableData method) (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringIntegerMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphContainer method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) (pyrosetta.rosetta.core.scoring.DipolarCoupling method) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.NCSResMapping method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) get_semirotameric() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_separated_interface_energy() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_separated_interface_energy_ratio() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_seq_design_options() (in module pyrosetta.rosetta.protocols.antibody.design) get_seq_sep() (in module pyrosetta.rosetta.core.scoring.hbonds) get_seq_sep_scale() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) get_sequence() (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) get_sequence_information() (in module pyrosetta.rosetta.core.import_pose) get_sequence_len() (in module pyrosetta.rosetta.core.pose) get_sequence_region() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) get_sfxn_cycles() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) get_sfxn_name() (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) get_sha1_hash_excluding_chain() (in module pyrosetta.rosetta.core.pose) get_sha1_hash_excluding_chains() (in module pyrosetta.rosetta.core.pose) get_sha1_hash_from_chain() (in module pyrosetta.rosetta.core.pose) get_sha1_hash_from_chains() (in module pyrosetta.rosetta.core.pose) get_shared_silent_data() (pyrosetta.rosetta.core.io.silent.SilentFileData method) get_sheet() (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) get_sheet_antiparallel_info() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_shell_radius() (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) get_short_backrub_mover() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_short_name_to_iupac_strings_map() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) get_side1_nres() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_side1_score() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_side2_nres() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_side2_score() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_side_from_num() (in module pyrosetta.rosetta.core.chemical.rna) get_sidechain_indices() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) get_sidechain_reference_frame() (in module pyrosetta.rosetta.core.pose.motif) get_sidechain_reference_frame_atomids() (in module pyrosetta.rosetta.core.pose.motif) get_sidechain_reference_frame_atomids_with_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_silent_energies() (pyrosetta.rosetta.core.io.silent.SilentStruct method) get_silent_energy() (pyrosetta.rosetta.core.io.silent.SilentStruct method) get_silent_file_tags() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) get_simple_node() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) get_single_rotamer_born_radii() (pyrosetta.rosetta.core.scoring.FACTSPotential method) get_size() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_size_sandwich_PK_id() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_slice_width() (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) get_slide_axis() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_smallest_glycan_tree_layer() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_smooth() (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) get_solution_picker() (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) get_spanfile() (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) get_spanfiles() (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) get_sparse_aa_info_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) get_species() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) get_specific_atom_coordinate() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) get_specific_module_name_as_it_appears_in_xsd() (in module pyrosetta.rosetta.utility.xsd_util) get_spectrum() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) get_spin_center() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_ss_cutoff() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) get_ss_lowstrand() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) get_ss_type() (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) get_ssbond_record() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) get_ssdep_weight() (in module pyrosetta.rosetta.core.scoring.hbonds) get_stability_metric() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_start() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) get_start_points() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_start_res() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) get_starting_res_for_connecting_strands() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_static_int() (pyrosetta.rosetta.utility.py.PyExitCallback method) get_static_string() (pyrosetta.rosetta.utility.py.PyExitCallback method) get_static_string_const() (pyrosetta.rosetta.utility.py.PyExitCallback method) get_stem_movemap() (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) get_stem_taskfactory() (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) get_stepsize() (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) get_stop_res() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) get_strand_dist_cutoff() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) get_strand_sew_models_from_db() (in module pyrosetta.rosetta.protocols.legacy_sewing) get_stretch_strand_dist_cutoff() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) get_strict_loops() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) get_string() (in module pyrosetta.rosetta.utility.json_spirit) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) get_string_comparison_type_strings() (in module pyrosetta.rosetta.protocols.simple_filters) get_string_from_property() (pyrosetta.rosetta.core.chemical.ResidueProperties method) get_string_from_variant() (pyrosetta.rosetta.core.chemical.ResidueProperties method) get_string_option() (in module pyrosetta.rosetta.basic.options) get_string_or_empty() (in module pyrosetta.rosetta.utility.json_spirit) get_string_property() (pyrosetta.rosetta.core.chemical.ResidueType method) get_string_real_pairs() (pyrosetta.rosetta.protocols.jd2.Job method) get_string_real_pairs_from_current_job() (in module pyrosetta.rosetta.protocols.jd2) get_string_string_pairs() (pyrosetta.rosetta.protocols.jd2.Job method) get_string_string_pairs_from_current_job() (in module pyrosetta.rosetta.protocols.jd2) get_string_value() (pyrosetta.rosetta.core.io.silent.SilentStruct method) get_string_vector_option() (in module pyrosetta.rosetta.basic.options) get_strings() (pyrosetta.rosetta.protocols.jd2.Job method) get_strings_from_current_job() (in module pyrosetta.rosetta.protocols.jd2) get_struct_id_with_highest_score_from_job_data() (in module pyrosetta.rosetta.protocols.features) get_struct_id_with_highest_score_from_score_data() (in module pyrosetta.rosetta.protocols.features) get_struct_id_with_lowest_score_from_job_data() (in module pyrosetta.rosetta.protocols.features) get_struct_id_with_lowest_score_from_score_data() (in module pyrosetta.rosetta.protocols.features) get_struct_id_with_nth_lowest_score_from_job_data() (in module pyrosetta.rosetta.protocols.features) get_struct_id_with_nth_lowest_score_from_score_data() (in module pyrosetta.rosetta.protocols.features) get_structure() (pyrosetta.rosetta.core.io.silent.SilentFileData method) get_stub() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) get_stub_from_residue() (in module pyrosetta.rosetta.core.conformation) get_stub_stub() (in module pyrosetta.rosetta.core.pose.rna) get_stub_transform() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) get_sub_score() (pyrosetta.rosetta.core.scoring.ScoreFunction method) get_sub_score_exclude_res() (pyrosetta.rosetta.core.scoring.ScoreFunction method) get_subcluster() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) get_subpose() (in module pyrosetta.rosetta.core.pose.symmetry) get_subset_from_residues() (in module pyrosetta.rosetta.core.select) get_subset_name() (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) get_subunit_name_to_component() (in module pyrosetta.rosetta.core.pose.symmetry) get_success() (pyrosetta.rosetta.protocols.LoopRebuild method) get_sugar_centroid() (in module pyrosetta.rosetta.core.pose.rna) get_sugar_torsions() (in module pyrosetta.rosetta.core.scoring.dna) get_suite_torsion_ids() (in module pyrosetta.rosetta.core.pose.rna) get_super_secret_fixed_interface_mode() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_superposition_transformation() (in module pyrosetta.rosetta.protocols.hybridization) get_surf_tot() (in module pyrosetta.rosetta.core.scoring.packing) get_surf_vol() (in module pyrosetta.rosetta.core.scoring.packing) get_surf_vol_deriv() (in module pyrosetta.rosetta.core.scoring.packing) get_surrounding_O2prime_hydrogen() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) get_sym_aware_jump_num() (in module pyrosetta.rosetta.core.pose.symmetry) get_sym_dof_names() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) get_symbols() (pyrosetta.rosetta.core.sequence.ABEGOManager method) get_symdof_subunits() (in module pyrosetta.rosetta.core.pose.symmetry) get_symm_axis() (in module pyrosetta.rosetta.core.pose.symmetry) get_symmops_Aba2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Abm2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Ama2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Amm2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_B11m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_C121() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_C12slashc1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_C12slashm1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_C1c1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_C1m1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_C222() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_C2221() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Ccc2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Ccca__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Cccm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Cmc21() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Cmca() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Cmcm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Cmm2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Cmma() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Cmmm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_F222() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_F23() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_F4132() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_F432() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fdd2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fddd__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fdminus3__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fdminus3c__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fdminus3m__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fminus43c() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fminus43m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fmm2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fmminus3() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fmminus3c() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fmminus3m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fmmm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I212121() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I213() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I222() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I23() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I4() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I41() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I4122() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I4132() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I41cd() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I41md() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I41slasha__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I41slashacd__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I41slashamd__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I422() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I432() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I4cm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I4mm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I4slashm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I4slashmcm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I4slashmmm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Iaminus3() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Iaminus3d() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Iba2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Ibam() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Ibca() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Ima2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Iminus4() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Iminus42d() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Iminus42m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Iminus43d() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Iminus43m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Iminus4c2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Iminus4m2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Imm2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Imma() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Imminus3() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Imminus3m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Immm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P121() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P1211() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P121slashc1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P121slashm1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P121slashn1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P12slashc1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P12slashm1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P1c1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P1m1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P21212() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P212121() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P213() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P222() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P2221() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P23() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P3() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P31() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P3112() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P312() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P3121() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P31c() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P31m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P32() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P321() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P3212() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P3221() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P3c1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P3m1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P41() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P41212() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4122() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4132() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4212() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P422() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42212() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4222() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4232() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42bc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42cm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42mc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42nm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42slashm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42slashmbc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42slashmcm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42slashmmc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42slashmnm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42slashn__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42slashnbc__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42slashncm__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42slashnmc__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42slashnnm__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P43() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P432() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P43212() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4322() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4332() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4bm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4cc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4mm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4nc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4slashm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4slashmbm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4slashmcc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4slashmmm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4slashmnc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4slashn__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4slashnbm__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4slashncc__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4slashnmm__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4slashnnc__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P61() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6122() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P62() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P622() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6222() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P63() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6322() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P63cm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P63mc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P63slashm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P63slashmcm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P63slashmmc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P64() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6422() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P65() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6522() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6cc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6mm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6slashm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6slashmcc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6slashmmm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Paminus3() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pba2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pbam() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pban__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pbca() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pbcm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pbcn() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pca21() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pcc2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pcca() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pccm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pccn() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pma2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pmc21() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus3() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus31c() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus31m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus3c1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus3m1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus4() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus421c() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus421m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus42c() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus42m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus43m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus43n() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus4b2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus4c2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus4m2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus4n2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus6() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus62c() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus62m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus6c2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus6m2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pmm2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pmma() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pmminus3() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pmminus3m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pmminus3n() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pmmm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pmmn__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pmn21() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pmna() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pna21() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pnc2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pnma() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pnminus3__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pnminus3m__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pnminus3n__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pnn2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pnna() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pnnm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pnnn__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_R32__H() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_R3__H() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_R3c__H() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_R3m__H() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Rminus3__H() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Rminus3c__H() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Rminus3m__H() (in module pyrosetta.rosetta.protocols.cryst) get_tag() (in module pyrosetta.rosetta.core.io.rna) (in module pyrosetta.rosetta.protocols.features.strand_assembly) (pyrosetta.rosetta.protocols.toolbox.KClusterData method) get_tag_and_silent_file_for_struct() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) get_tag_from_pdb_filename() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) get_tag_name() (in module pyrosetta.rosetta.utility.xsd_util) get_tag_score_map() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) get_tags() (in module pyrosetta.rosetta.core.io.rna) get_tailfunction_from_name() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup method) get_tailfunction_name() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup method) get_target_atom_name() (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) get_target_position_map_make_dna_mutations() (in module pyrosetta.rosetta.protocols.motifs) get_target_positions_make_dna_mutations() (in module pyrosetta.rosetta.protocols.motifs) get_target_residue() (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) get_targetconformers_user() (in module pyrosetta.rosetta.protocols.motifs) get_task() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_task_factory() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) get_task_operation_names_from_xsd() (in module pyrosetta.rosetta.utility.xsd_util) get_task_operations() (in module pyrosetta.rosetta.core.pack.task) get_TaskFactory_AllCDRs() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_TaskFactory_OneCDR() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_temp_cycles() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) get_temperature() (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_template_atoms_at_pos() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) get_tenA_neighbor_residues() (in module pyrosetta.rosetta.core.select) get_termini_from_pose() (in module pyrosetta.rosetta.protocols.sic_dock) get_third_atom() (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) get_third_offset() (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) get_this_filter_type_name() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) get_threshold() (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) get_time() (in module pyrosetta.rosetta.protocols.wum) get_timer() (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) get_tips() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) get_tm_alpha() (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) get_token() (in module pyrosetta.rosetta.core.pack.task) get_tolerance() (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) get_top_designs() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) get_torsion() (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) get_torsion_angle_atom_ids() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) get_torsion_bin() (in module pyrosetta.rosetta.core.conformation) get_torsion_mean() (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) get_torsion_sd() (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) get_torsion_type() (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) get_torsions() (in module pyrosetta.rosetta.protocols.recces) (in module pyrosetta.rosetta.protocols.recces.scratch) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) get_torsions_for_all_solutions() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) get_total() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) get_total_base_axis_score() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) get_total_base_pair_score() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) get_total_base_stack_axis_score() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) get_total_base_stack_score() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) get_total_base_stagger_score() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) get_total_dots() (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) get_total_Hbond_E() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_total_hsasa() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_total_hsasa_bb() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_total_hsasa_sc() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_total_mutation_sets() (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) get_total_num_CDRs() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_total_rel_hsasa() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_total_sasa() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_total_sasa_bb() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_total_sasa_sc() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_touched_res() (in module pyrosetta.rosetta.protocols.mpi_refinement) get_trans_mag() (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) get_trans_magnitude() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) get_transformation() (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) get_translation() (pyrosetta.rosetta.core.kinematics.Jump method) get_translation_magnitude() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_tree() (in module pyrosetta.rosetta.core.import_pose) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_tree_containing_residue() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_tree_map() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_tree_root_of_glycan_residue() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_tree_start_of_glycan_residue() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_trie() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) get_two_body_energy_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) get_type() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) get_type_difference_name() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_type_info() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap method) get_type_name() (in module pyrosetta.rosetta.utility.xsd_util) get_unbound_mode() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_unbound_mut_pose() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) get_unbound_wt_pose() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) get_undefined_real() (in module pyrosetta.rosetta.utility) get_undefined_size() (in module pyrosetta.rosetta.utility) get_unfoled_potential_file_weights() (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential method) get_uniform_backrub() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_unique_connection_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_unrecognized_atoms() (pyrosetta.rosetta.core.pose.PDBInfo method) get_unrecognized_res_name() (pyrosetta.rosetta.core.pose.PDBInfo method) get_unrecognized_res_size() (pyrosetta.rosetta.core.pose.PDBInfo method) get_update_boinc() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) get_upper_cutpoint_partner_for_lower() (in module pyrosetta.rosetta.core.scoring.methods) get_usage_from_procfilesystem() (in module pyrosetta.rosetta.basic) get_use_centroid_dG() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_use_contact_selector() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_use_ligand_selector() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_use_lowest() (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) get_use_tracer() (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) get_useful_HOH_coords() (in module pyrosetta.rosetta.protocols.magnesium) get_user_defined_name() (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) get_using_a_resselect() (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) get_valence_electrons_sp() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_Vall() (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager method) get_vall() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_vall_by_key() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) get_vall_count() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) get_vall_end_line_by_key() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) get_vall_filename() (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) get_vall_last_residue_key_by_key() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) get_vall_middle_res_id() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) get_vall_provider() (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) get_vall_start_line_by_key() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) get_value() (in module pyrosetta.rosetta.utility.json_spirit) get_variant_from_string() (pyrosetta.rosetta.core.chemical.ResidueProperties method) get_vary_bondangles() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) get_VdRdPhi() (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) get_VDW_weight() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_vec_AA_kind() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_vec_distinct_sheet_id() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_vec_of_sw_can_by_sh_id() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_vector_of_loop_AA_distribution() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_vector_of_strand_AA_distribution() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_vertex_member_of_energy_sum_group() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) get_voxel_coordinates() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) get_water_res() (in module pyrosetta.rosetta.protocols.magnesium) get_water_uniform_rotation_sampler() (in module pyrosetta.rosetta.protocols.magnesium) get_watson_crick_base_pair_atoms() (in module pyrosetta.rosetta.core.chemical.rna) get_WC_atom() (in module pyrosetta.rosetta.core.chemical.rna) get_weight() (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 method) get_weights() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) get_weights_for_one_partner_hbonder() (in module pyrosetta.rosetta.core.scoring.hbonds) get_weights_for_two_partner_hbonder() (in module pyrosetta.rosetta.core.scoring.hbonds) get_work_unit() (pyrosetta.rosetta.protocols.wum.WorkUnitList method) get_work_unit_clone() (pyrosetta.rosetta.protocols.wum.WorkUnitList method) get_working_directory() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) get_wu_type() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) get_xform_stats() (in module pyrosetta.rosetta.protocols.sic_dock) get_xml_schema_attributes() (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) get_xsd_complex_type() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) get_y_axis() (in module pyrosetta.rosetta.core.scoring.dna) get_y_axis_atoms() (in module pyrosetta.rosetta.core.scoring.dna) get_z_axis() (in module pyrosetta.rosetta.core.scoring.dna) get_zeta_cutoff() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) GetAtoms() (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) getAVG() (in module pyrosetta.rosetta.protocols.sparta) getBounds() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) getCoordinateTransformation() (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) getDensityMap() (in module pyrosetta.rosetta.core.scoring.electron_density) getDensityMap_legacy() (in module pyrosetta.rosetta.core.scoring.electron_density) getDiff() (in module pyrosetta.rosetta.protocols.sparta) GetDots() (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) getFiberDiffractionData() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) getFiberDiffractionData_legacy() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) getLargestClusterSize() (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) getline() (in module pyrosetta.rosetta.ObjexxFCL) (in module pyrosetta.rosetta.utility.io) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) getListNames() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) getMapSpacingAndOrigin() (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) GetMaximumElectrons() (pyrosetta.rosetta.core.chemical.Bond method) GetMinimumElectrons() (pyrosetta.rosetta.core.chemical.Bond method) getMLweight() (in module pyrosetta.rosetta.core.util) getMLweight_cart() (in module pyrosetta.rosetta.core.util) GetMostStableType() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) getNeighbors() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) getNetClusterSize() (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) GetNumberOfElectrons() (pyrosetta.rosetta.core.chemical.Bond method) GetNumberPossibleTypes() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) getPdbCodes() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) getPdbNames() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) getPhenixInterface() (in module pyrosetta.rosetta.core.scoring.cryst) getPose() (pyrosetta.rosetta.core.pose.signals.ConformationEvent method) (pyrosetta.rosetta.core.pose.signals.EnergyEvent method) (pyrosetta.rosetta.core.pose.signals.GeneralEvent method) getPoseExtraScore() (in module pyrosetta.rosetta.core.pose) GetPropertyName() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) getRandom() (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) GetRBDOFValues (class in pyrosetta.rosetta.protocols.matdes) getRelaxResidues() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) getResidueRange() (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) GetResults() (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) getRMS() (in module pyrosetta.rosetta.protocols.sparta) GetSDAltFileID() (pyrosetta.rosetta.core.chemical.Bond method) GetSDFileID() (pyrosetta.rosetta.core.chemical.Bond method) getSecStruct() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) getSeed() (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) getSigAxisR() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) getSigAxisT() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) getSigOffAxisR() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) getSigOffAxisT() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) getSTD() (in module pyrosetta.rosetta.protocols.sparta) getTotalMemoryUsage() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) getValues() (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) getxform() (in module pyrosetta.rosetta.core.fragment) (in module pyrosetta.rosetta.protocols.sic_dock) ghost_loops() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) give_dihedral_index() (in module pyrosetta.rosetta.protocols.ncbb) global2local() (pyrosetta.rosetta.core.kinematics.Stub method) global_loop_rmsd() (in module pyrosetta.rosetta.protocols.antibody) global_mapping() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) global_offset() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) global_optimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) global_rotamer_id() (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) global_sequence() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) GlobalResidueTypeSet (class in pyrosetta.rosetta.core.chemical) glu_corrections() (in module pyrosetta.rosetta.protocols.make_rot_lib) glycam_pdb_format() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) glycan_tree_set() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) GlycanInfoMover (class in pyrosetta.rosetta.protocols.analysis) GlycanLayerSelector (class in pyrosetta.rosetta.core.select.residue_selector) GlycanNode (class in pyrosetta.rosetta.core.conformation.carbohydrates) GlycanRelaxMover (class in pyrosetta.rosetta.protocols.carbohydrates) GlycanResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) GlycanSequon (class in pyrosetta.rosetta.protocols.carbohydrates) GlycanSequonsSelector (class in pyrosetta.rosetta.core.select.residue_selector) GlycanTree (class in pyrosetta.rosetta.core.conformation.carbohydrates) GlycanTreeMinMover (class in pyrosetta.rosetta.protocols.carbohydrates) GlycanTreeRelax (class in pyrosetta.rosetta.protocols.carbohydrates) GlycanTreeSet (class in pyrosetta.rosetta.core.conformation.carbohydrates) GlycanTreeSetObserver (class in pyrosetta.rosetta.core.conformation.carbohydrates) glycosylate_pose() (in module pyrosetta.rosetta.core.pose.carbohydrates) glycosylate_pose_by_file() (in module pyrosetta.rosetta.core.pose.carbohydrates) GlycosyltransferaseMover (class in pyrosetta.rosetta.protocols.enzymatic_movers) GlycosyltransferaseMoverCreator (class in pyrosetta.rosetta.protocols.enzymatic_movers) go() (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringProtocol method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) GoapEnergy (class in pyrosetta.rosetta.core.scoring.methods) GoapRsdType (class in pyrosetta.rosetta.core.scoring.methods) good() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) grab_additional_pose_data() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) grab_main_chain_torsion_set_list() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) grab_pose_cache_data() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) grab_pose_energies_table() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) GrabAllCollector (class in pyrosetta.rosetta.protocols.frag_picker) gradnorm() (in module pyrosetta.rosetta.numeric.crick_equations) graft_cdr_loops() (in module pyrosetta.rosetta.protocols.antibody.grafting) graft_closed() (in module pyrosetta.rosetta.protocols.grafting) GraftedStemOptimizer (class in pyrosetta.rosetta.protocols.antibody) GraftMover (class in pyrosetta.rosetta.protocols.antibody_legacy) GraftMoverBase (class in pyrosetta.rosetta.protocols.grafting) GraftOneCDRLoop (class in pyrosetta.rosetta.protocols.antibody) GraftOneMover (class in pyrosetta.rosetta.protocols.antibody_legacy) Graph (class in pyrosetta.rosetta.utility.graph) graph() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphContainer method) greedy_around() (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) GreedyKCenter (class in pyrosetta.rosetta.protocols.toolbox) greek_distance() (pyrosetta.rosetta.core.chemical.Atom method) GreekDistance (class in pyrosetta.rosetta.core.chemical) grid_rotamer_trials() (in module pyrosetta.rosetta.protocols.ligand_docking) grid_rotamer_trials_atr_rep() (in module pyrosetta.rosetta.protocols.ligand_docking) grid_score() (in module pyrosetta.rosetta.protocols.ligand_docking) grid_score_atr_rep() (in module pyrosetta.rosetta.protocols.ligand_docking) grid_scores() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) GridCreator (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) GriddedAtomTreeMultifunc (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) GridSet (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) group1_resstring() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) group1_selector() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) group1_set() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) group2_resstring() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) group2_selector() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) group2_set() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) group_heavyatom_index_to_group_index() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) group_id() (pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator method) group_name() (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) GroupDiscriminator (class in pyrosetta.rosetta.protocols.minimization_packing) groups() (pyrosetta.rosetta.protocols.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) grow() (in module pyrosetta.rosetta.protocols.ligand_docking) grow_all_loops() (pyrosetta.rosetta.protocols.loops.Loops method) grow_left_r() (in module pyrosetta.rosetta.protocols.forge.methods) grow_loop() (pyrosetta.rosetta.protocols.loops.Loops method) grow_loop_away_from_sheets() (pyrosetta.rosetta.protocols.loops.Loops method) grow_right_r() (in module pyrosetta.rosetta.protocols.forge.methods) GrowLeft (class in pyrosetta.rosetta.protocols.forge.build) GrowRight (class in pyrosetta.rosetta.protocols.forge.build) grp_cpfxn() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) grpelec_context_dependent() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) grpelec_fade_hbond() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) grpelec_fade_param1() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) grpelec_fade_param2() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) grpelec_fade_type() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) GT_Expression (class in pyrosetta.rosetta.numeric.expression_parser) GTE_Expression (class in pyrosetta.rosetta.numeric.expression_parser) guarantee_no_DNA() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) GuardedLoopsFromFile (class in pyrosetta.rosetta.protocols.loops) guess_rbsegs_from_pose() (in module pyrosetta.rosetta.protocols.rbsegment_relax) GunnCostScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) gunzip() (in module pyrosetta.rosetta.utility.file) gzip() (in module pyrosetta.rosetta.core.io.silent) (in module pyrosetta.rosetta.utility.file) gzipped() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method)

H

H1_pattern() (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager method) h1_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) h2_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) h2o_hbond_score_1way() (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) h3_base_type_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) h3_base_type_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) H3_pattern() (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager method) h3_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) H3BaseTypeEnum (class in pyrosetta.rosetta.protocols.antibody) H3CterInsert (class in pyrosetta.rosetta.protocols.antibody) H_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) HA_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) HACK_dump_helices() (in module pyrosetta.rosetta.core.scoring.motif) HACK_dump_helix() (in module pyrosetta.rosetta.core.scoring.motif) Hairpin (class in pyrosetta.rosetta.core.scoring) hairpins() (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) halfbin6() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) halfbin_widths() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) HamiltonianExchangeCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) handle_function_expression() (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) handle_structured_xml_error() (in module pyrosetta.rosetta.utility.tag) handle_variable_expression() (pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser method) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) handle_xml_error() (in module pyrosetta.rosetta.utility.tag) handle_xml_warning() (in module pyrosetta.rosetta.utility.tag) handles_metric_value() (in module pyrosetta.rosetta.basic) hankel_free() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) hankel_get_p0() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) hankel_get_rc() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) hankel_in_machine() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) hankel_make_j() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) hankel_make_rp() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) hankel_make_snn() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) hankel_r_div() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) hankel_r_mult() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) hankel_set_alpha() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) hankel_trans_no_lec() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) Haro_index() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) has() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.ConstDataMap method) (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap method) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.NoFailDataMap method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.utility.options.OptionCollection method) has_algorithm() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) has_another_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) has_any_false_selection() (in module pyrosetta.rosetta.core.select.residue_selector) has_any_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) has_any_of_characters() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) has_any_true_selection() (in module pyrosetta.rosetta.core.select.residue_selector) has_atom() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) has_atom_info() (pyrosetta.rosetta.core.kinematics.Edge method) has_been_instantiated() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) has_behavior() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) has_C_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) has_CA_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) has_cached_data() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) has_CB_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) has_CDR() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) has_chain() (in module pyrosetta.rosetta.core.pose) has_chemical_shifts() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) has_cluster_for_cdr() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) has_comment() (pyrosetta.rosetta.core.io.silent.SilentStruct method) has_common_pairing() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) has_connected_resonances() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) has_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) has_coordinates() (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) has_custom_variant_types() (pyrosetta.rosetta.core.chemical.ResidueProperties method) has_default() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) has_dependencies() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) has_dof() (pyrosetta.rosetta.core.pose.Pose method) has_dof_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) has_domain() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) has_energy() (pyrosetta.rosetta.core.io.silent.SilentStruct method) has_evaluator() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) has_exocyclic_glycosidic_linkage() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) has_exocyclic_linkage() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) has_extra_parameter() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) has_file_contents() (pyrosetta.rosetta.utility.io.FileContentsMap method) has_finished() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) has_framework_dependant_cluster() (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) has_framework_dependant_clusters() (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) has_free_lower_terminus() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) has_free_upper_terminus() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) has_glycan_residue() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) has_grid() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) has_H_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) has_HA_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) has_incomplete_connection() (pyrosetta.rosetta.core.conformation.Residue method) has_incomplete_connections() (in module pyrosetta.rosetta.protocols.ligand_docking) has_insertion_operator() (in module pyrosetta.rosetta.utility.type_traits) has_interchangeability_group() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) has_intra_residue_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) has_job() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) has_job_completed() (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) has_label() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) has_lower_connect() (pyrosetta.rosetta.core.conformation.Residue method) has_lower_residue() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) has_metapatch() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) has_method_weights() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) has_N_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) has_name() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) has_name3() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) has_native_sequence() (in module pyrosetta.rosetta.protocols.antibody.design) has_next() (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) has_node() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) has_node_corresponding_to_residue() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) has_non_residue_pair_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) has_nonzero_weight() (pyrosetta.rosetta.core.scoring.ScoreFunction method) has_O_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) has_observer() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) has_omega() (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) has_open_slaves() (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) has_orbital() (pyrosetta.rosetta.core.chemical.ResidueType method) has_orbitals() (pyrosetta.rosetta.core.chemical.Atom method) has_orientation_and_pleating() (in module pyrosetta.rosetta.core.scoring.dssp) has_pairing() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) has_parent_remark() (pyrosetta.rosetta.core.io.silent.SilentStruct method) has_passport() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) has_polymer_dependent_groups() (pyrosetta.rosetta.core.chemical.ResidueType method) has_prefix() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) has_previous() (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) has_profile() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) has_profile_struct() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) has_property() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) has_proton() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) has_reactivities() (pyrosetta.rosetta.core.io.rna.RNA_DataReader method) has_read_limit_for_file() (pyrosetta.rosetta.utility.io.FileContentsMap method) has_ref_pose() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) has_ref_tag() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) has_reference_pose() (pyrosetta.rosetta.core.pose.Pose method) has_res_type_set() (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) has_residue() (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) has_residue_pair_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) has_residue_selector() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) has_residue_type_set() (pyrosetta.rosetta.core.chemical.ChemicalManager method) has_resource() (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.NoFailDataMap method)

has_resource_loader() (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) has_restype() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) has_rna_secstruct_legacy() (in module pyrosetta.rosetta.core.pose.rna.secstruct_legacy) has_sc_orbitals() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) has_segment() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) has_severe_pep_bond_geom_issues() (in module pyrosetta.rosetta.protocols.loops) has_shadow_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) has_shared_silent_data() (pyrosetta.rosetta.core.io.silent.SilentFileData method) has_silent_in() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) has_stored_constraints() (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) has_suffix() (in module pyrosetta.rosetta.ObjexxFCL) has_tag() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) has_template() (pyrosetta.rosetta.core.import_pose.libraries.RNA_JumpLibrary method) has_template_pose() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) has_top_level_element() (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) has_tree() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) has_type() (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.NoFailDataMap method) has_upper_connect() (pyrosetta.rosetta.core.conformation.Residue method) has_upper_residue() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) has_upstream_only_geomcsts() (pyrosetta.rosetta.protocols.match.Matcher method) has_value() (in module pyrosetta.rosetta.utility.json_spirit) (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepLibrary method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) has_variant_type() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) has_virtual_rna_residue_variant_type() (in module pyrosetta.rosetta.core.pose.rna) has_zero_weight() (pyrosetta.rosetta.core.scoring.ScoreFunction method) hASA_patch_energy() (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) hash() (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) hash_fingerprint() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) hash_model() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) hash_value() (in module pyrosetta.rosetta.protocols.abinitio) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) HashEdge (class in pyrosetta.rosetta.protocols.legacy_sewing) Hasher (class in pyrosetta.rosetta.protocols.legacy_sewing) hasPoseExtraScore() (in module pyrosetta.rosetta.core.pose) hasPoseExtraScore_str() (in module pyrosetta.rosetta.core.pose) have_mutated_residue() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) hb_energy() (in module pyrosetta.rosetta.core.scoring.hbonds) hb_energy_deriv() (in module pyrosetta.rosetta.core.scoring.hbonds) hb_energy_deriv_u() (in module pyrosetta.rosetta.core.scoring.hbonds) hb_energy_deriv_u2() (in module pyrosetta.rosetta.core.scoring.hbonds) hb_eval_type() (in module pyrosetta.rosetta.core.scoring.hbonds) hb_eval_type_weight() (in module pyrosetta.rosetta.core.scoring.hbonds) HBAccChemType (class in pyrosetta.rosetta.core.scoring.hbonds) HBDefType (class in pyrosetta.rosetta.protocols.features) HBDerivType (class in pyrosetta.rosetta.core.scoring.hbonds) HBDonChemType (class in pyrosetta.rosetta.core.scoring.hbonds) hbe_is_BB_type() (in module pyrosetta.rosetta.core.scoring.hbonds) hbe_is_SC_type() (in module pyrosetta.rosetta.core.scoring.hbonds) HBEvalType (class in pyrosetta.rosetta.core.scoring.hbonds) HBGeoDimType (class in pyrosetta.rosetta.core.scoring.hbonds) hbnet_bonus_function_ramping() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) hbnet_energy_ramping_enum_from_string() (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) hbnet_energy_ramping_string_from_enum() (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) hbnet_max_network_size() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) hbnet_one_body_energies() (in module pyrosetta.rosetta.protocols.hbnet) hbnet_symm_one_body_energies() (in module pyrosetta.rosetta.protocols.hbnet) HBNetEnergy (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy) HBNetEnergyRamping (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy) hbond() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) hbond_compute_energy() (in module pyrosetta.rosetta.core.scoring.hbonds) hbond_cop() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) hbond_database() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) hbond_energy_cutoff() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) hbond_energy_threshold() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions method) hbond_evaluation_type() (in module pyrosetta.rosetta.core.scoring.hbonds) hbond_exists_in_vector() (in module pyrosetta.rosetta.protocols.hbnet) hbond_options() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) hbond_weight() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) hbonded() (in module pyrosetta.rosetta.protocols.protein_interface_design) hbonded_atom() (in module pyrosetta.rosetta.protocols.protein_interface_design) HBondFeaturesCreator (class in pyrosetta.rosetta.protocols.features) hbonding_to_res() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) HBondNetStruct (class in pyrosetta.rosetta.protocols.hbnet) HBondParameterFeaturesCreator (class in pyrosetta.rosetta.protocols.features) HBondResStruct (class in pyrosetta.rosetta.protocols.hbnet) hbonds() (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) HBondSet (class in pyrosetta.rosetta.core.scoring.hbonds) HbondsToAtomFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) HbondsToResidueFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) HBondWeightType (class in pyrosetta.rosetta.core.scoring.hbonds) HBSeqSep (class in pyrosetta.rosetta.core.scoring.hbonds) head() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) head_of_queue() (pyrosetta.rosetta.utility.recent_history_queue method) header() (pyrosetta.rosetta.core.io.StructFileRep method) header_from_atom_tree_diff() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) header_information() (pyrosetta.rosetta.core.pose.PDBInfo method) HeaderInformation (class in pyrosetta.rosetta.core.io) HeaderInformation.CompoundToken (class in pyrosetta.rosetta.core.io) HeaderInformation.ExperimentalTechnique (class in pyrosetta.rosetta.core.io) heap_down() (in module pyrosetta.rosetta.protocols.frags) heap_extract() (in module pyrosetta.rosetta.protocols.frags) heap_init() (in module pyrosetta.rosetta.protocols.frags) heap_insert() (in module pyrosetta.rosetta.protocols.frags) heap_replace() (in module pyrosetta.rosetta.protocols.frags) heap_up() (in module pyrosetta.rosetta.protocols.frags) heat_after_cycles() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) heavy_atom_names_match() (in module pyrosetta.rosetta.core.chemical) heavy_framework() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) heavyatom_has_polar_hydrogens() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) heavyatom_index() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) heavyatom_is_an_acceptor() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) HeavyAtomFilter (class in pyrosetta.rosetta.core.chemical) heavyAtoms_end() (pyrosetta.rosetta.core.conformation.Residue method) HeavyAtomWithHydrogensFilter (class in pyrosetta.rosetta.core.chemical) HeavyAtomWithPolarHydrogensFilter (class in pyrosetta.rosetta.core.chemical) HelicalGaussianMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) Helices (class in pyrosetta.rosetta.core.scoring) helices() (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) Helix (class in pyrosetta.rosetta.protocols.fldsgn.topology) helix() (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) helix_fraction() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) helix_id() (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) helix_index() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) helix_pairing() (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) helix_pairings() (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) HelixArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) HelixBendFilter (class in pyrosetta.rosetta.protocols.fldsgn.filters) HelixBundleFeaturesCreator (class in pyrosetta.rosetta.protocols.features.helixAssembly) HelixCapFeaturesCreator (class in pyrosetta.rosetta.protocols.features) HelixFromSequence (class in pyrosetta.rosetta.protocols.membrane) HELIXInformation (class in pyrosetta.rosetta.core.io) HELIXInformations() (pyrosetta.rosetta.core.io.StructFileRep method) HelixPairingSet (class in pyrosetta.rosetta.protocols.fldsgn.topology) HelixPerturber (class in pyrosetta.rosetta.protocols.denovo_design.components) HelixRotate (class in pyrosetta.rosetta.protocols.nonlocal) helper() (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) heterogen_formulae() (pyrosetta.rosetta.core.io.StructFileRep method) heterogen_names() (pyrosetta.rosetta.core.io.StructFileRep method) heterogen_synonyms() (pyrosetta.rosetta.core.io.StructFileRep method) HierarchicalDataMap (class in pyrosetta.rosetta.basic.datacache) high_res() (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) high_res_kink_constraint() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) high_temp() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) higher_numbered_node_symmetry_copy_index() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond method) highest_job_index() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) highest_probability() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) highres_reference_energy() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) highval() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) hijack_loop_reading_code_set_loop_line_begin_token() (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader method) his_tyr_connectivity() (in module pyrosetta.rosetta.protocols.hbnet) history_queue_struct (class in pyrosetta.rosetta.core.pack.interaction_graph) history_size() (pyrosetta.rosetta.utility.recent_history_queue method) hit_list_begin() (pyrosetta.rosetta.protocols.match.Matcher method) hit_list_end() (pyrosetta.rosetta.protocols.match.Matcher method) HitHasher (class in pyrosetta.rosetta.protocols.match) HitNeighborFinder (class in pyrosetta.rosetta.protocols.match) hits() (pyrosetta.rosetta.protocols.match.Matcher method) ho2prime_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) hokey_template_workaround() (in module pyrosetta.rosetta.numeric.interpolation.spline) HolesResult (class in pyrosetta.rosetta.core.scoring.packing) host_chain() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) hpatch_score() (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) HPatchEnergy (class in pyrosetta.rosetta.core.pack.interaction_graph) Hpol_index() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) Hpos_apolar() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) Hpos_polar() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) Hpos_polar_sc() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) hr_intersects_hs() (in module pyrosetta.rosetta.numeric.kdtree) HSPairPotential (class in pyrosetta.rosetta.protocols.fldsgn.potentials.sspot) hsv_to_rgb() (in module pyrosetta.rosetta.numeric) ht_for_chitip_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) ht_for_chitip_atoms() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) human_readable_summary() (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) hurry() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) Hybridization (class in pyrosetta.rosetta.core.chemical) hybridization() (pyrosetta.rosetta.core.chemical.AtomType method) hybridization_rank() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) hydrate_cavities() (in module pyrosetta.rosetta.protocols.hydrate) hydrate_hyfile() (in module pyrosetta.rosetta.protocols.hydrate) hydrate_magnesiums() (in module pyrosetta.rosetta.protocols.magnesium) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) hydrogen_interaction_cutoff2() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) HydrogenAtomFilter (class in pyrosetta.rosetta.core.chemical) HydrogenBondConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) HydrogenBondInfo (class in pyrosetta.rosetta.protocols.constraint_generator) hydrophobic_constraint_strength() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) HydrophobicityProfileSimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) HydrophobicitySimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) hyper_tan() (in module pyrosetta.rosetta.numeric.kinematic_closure)

I

I() (in module pyrosetta.rosetta.ObjexxFCL.format) i() (pyrosetta.rosetta.core.pose.rna.BasePairStep method) i2() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) i3() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) i_next() (pyrosetta.rosetta.core.pose.rna.BasePairStep method) IACHAR() (in module pyrosetta.rosetta.ObjexxFCL) ICHAR() (in module pyrosetta.rosetta.ObjexxFCL) iCode() (pyrosetta.rosetta.core.io.ResidueInformation method) icode() (pyrosetta.rosetta.core.pose.PDBInfo method) icoor() (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) ICoorAtomID (class in pyrosetta.rosetta.core.chemical) ICoorAtomID.Type (class in pyrosetta.rosetta.core.chemical) icstream (class in pyrosetta.rosetta.utility.io) id() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) id_for_current_rotamer() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) idate() (in module pyrosetta.rosetta.ObjexxFCL) idCode() (pyrosetta.rosetta.core.io.HeaderInformation method) ideal_bond_length_set() (pyrosetta.rosetta.core.chemical.ChemicalManager method) ideal_score() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) ideal_val() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) ideal_xyz() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.Orbital method) IdealAbegoGenerator (class in pyrosetta.rosetta.protocols.denovo_design.components) IdealBondLengthSet (class in pyrosetta.rosetta.core.chemical) idealize_combined_pose() (in module pyrosetta.rosetta.protocols.grafting) idealize_hydrogens() (in module pyrosetta.rosetta.core.conformation) idealize_insert() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) idealize_last_n_glycans_in_pose() (in module pyrosetta.rosetta.core.pose.carbohydrates) idealize_loop() (in module pyrosetta.rosetta.protocols.loops) idealize_position() (in module pyrosetta.rosetta.core.conformation) idealize_proline_nvs() (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) idealize_sidechains() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) IdealizeAnomericHydrogens (class in pyrosetta.rosetta.protocols.carbohydrates) IdealizeMover (class in pyrosetta.rosetta.protocols.idealize) IdealizeNonPhiPsi (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) IdealParameters (class in pyrosetta.rosetta.protocols.kinematic_closure) IdealParametersDatabase (class in pyrosetta.rosetta.core.scoring.methods) identical_info_consistency_check() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) identifier() (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) identify_and_set_cdr_cluster() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) identify_hbonds_1way() (in module pyrosetta.rosetta.core.scoring.hbonds) identify_hbonds_1way_AHdist() (in module pyrosetta.rosetta.core.scoring.hbonds) identify_hbonds_1way_membrane() (in module pyrosetta.rosetta.core.scoring.hbonds) identify_intra_res_hbonds() (in module pyrosetta.rosetta.core.scoring.hbonds) identify_sheet_id_by_residue_end() (in module pyrosetta.rosetta.protocols.features.strand_assembly) identities() (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation method) identity() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) identity_transform() (pyrosetta.rosetta.core.kinematics.Jump method) IdentityEval (class in pyrosetta.rosetta.core.fragment.picking_old.vall.eval) IdentityEvent (class in pyrosetta.rosetta.core.conformation.signals) IdentityEvent.Tag (class in pyrosetta.rosetta.core.conformation.signals) idle() (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) if_late_scoring_for_zeros() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) ifft3() (in module pyrosetta.rosetta.numeric.fourier) ifft3_dynamic() (in module pyrosetta.rosetta.numeric.fourier) IfThenFilter (class in pyrosetta.rosetta.protocols.filters) ig() (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) IGEdgeReweightContainer (class in pyrosetta.rosetta.core.pack.task) IGEdgeReweighter (class in pyrosetta.rosetta.core.pack.task) IGEdgeReweights() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) ignore() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) ignore_cmdline_enzdes_cstfile() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) ignore_default_task() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) ignore_light_chain() (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) ignore_residues_in_csts() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) ignore_sugars() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) ignore_unconnected_upper() (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) ignore_unrecognized_res() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) ignore_waters() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) ignore_zero_occupancy() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) ignored() (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) ignorefinished() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) import() (pyrosetta.rosetta.core.kinematics.MoveMap method) import_false() (pyrosetta.rosetta.core.kinematics.MoveMap method) import_pose_from_silent_file() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) import_tags() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) import_true() (pyrosetta.rosetta.core.kinematics.MoveMap method) ImportPoseOptions (class in pyrosetta.rosetta.core.import_pose) impose_constraints() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) improper_dihedral() (pyrosetta.rosetta.core.chemical.ResidueType method) improper_dihedrals_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) in_a_submotif() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) in_a_submotif_seed() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) in_blacklist() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) in_charge() (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) in_membrane() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) in_ngbat_sphere() (in module pyrosetta.rosetta.protocols.neighbor) in_nrg_graph() (in module pyrosetta.rosetta.protocols.neighbor) in_paired_strands() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) include_all_water() (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) include_current() (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) include_gly() (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) include_lips() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) include_native_aa() (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) include_native_restype() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) include_neighbors() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) include_only_center_clusters() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_clusters() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_clusters_add() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_clusters_clear() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_current_cluster() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_germlines() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_germlines_add() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_germlines_clear() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_pdbs() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_pdbs_add() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_pdbs_clear() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_species() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_species_add() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_species_clear() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_resid() (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) include_residue() (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) include_trp() (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation method) include_virtual_side_chain() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) incoming_message_queue_is_empty() (pyrosetta.rosetta.utility.SimulateMPI method) incomplete() (pyrosetta.rosetta.core.chemical.ResConnID method) increase_multi_cool_annealer_history_size() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) increase_packer_residue_radius() (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) increasing() (pyrosetta.rosetta.protocols.loops.Loop method) increment_accepted_hbond_count_for_group() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) increment_both() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) increment_both_and_cache() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) increment_client_rank() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) increment_counts() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) increment_cur_indices() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) increment_donated_hbond_count_for_group() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) increment_edge_list_iterator() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) increment_from_cached() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) increment_hbond_energy() (in module pyrosetta.rosetta.core.scoring.hbonds) increment_npd_hbond_energy() (in module pyrosetta.rosetta.core.scoring.hbonds) increment_nread_limit() (pyrosetta.rosetta.utility.io.FileContentsMap method) increment_reference_pose_mapping_after_seqpos() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) increment_self_overlap() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) increment_this_and_cache() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) indel_motif() (in module pyrosetta.rosetta.protocols.evolution.AlignmentCleanerTools) indel_motif_radius() (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) indel_motif_seq_id() (in module pyrosetta.rosetta.protocols.evolution.AlignmentCleanerTools) indent_w_spaces() (in module pyrosetta.rosetta.utility.tag) independent_cycles() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) IndependentBBTorsionSRFD (class in pyrosetta.rosetta.core.fragment) index() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.core.chemical.ResidueConnection method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) index2symbol() (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.core.sequence.SSManager method) index2symbolString() (pyrosetta.rosetta.core.sequence.SSManager method) IndexRange (class in pyrosetta.rosetta.ObjexxFCL) indicate_required_context_graphs() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) induced_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) induced_rf_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) info() (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) inherit_scorefxn_temperature() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) ini_func1() (in module pyrosetta.rosetta.numeric.random) ini_func2() (in module pyrosetta.rosetta.numeric.random) init() (in module pyrosetta) (in module pyrosetta.rosetta.basic) (in module pyrosetta.rosetta.core.init) (in module pyrosetta.rosetta.protocols.init) (pyrosetta.rosetta.basic.TracerImpl method) Init() (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) init() (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) init_angle() (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) init_bbgmover() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) init_beta_correction() (in module pyrosetta.rosetta.core.init) init_beta_july15_correction() (in module pyrosetta.rosetta.core.init) init_beta_nov16_correction() (in module pyrosetta.rosetta.core.init) init_common_options() (in module pyrosetta.rosetta.protocols.ncbb) init_correct_correction() (in module pyrosetta.rosetta.core.init) init_crystal_refinement_correction() (in module pyrosetta.rosetta.core.init) init_cst_score_types() (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) init_disp() (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) init_dna_correction() (in module pyrosetta.rosetta.core.init) init_facts_correction() (in module pyrosetta.rosetta.core.init) init_from_cmd() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) init_from_comand_line() (pyrosetta.rosetta.core.pack.task.operation.OptH method) init_from_decoy_set() (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) init_from_file() (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) init_from_lines() (pyrosetta.rosetta.core.io.silent.SilentStruct method) init_from_options() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) init_from_pose() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) init_from_vector() (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) init_gen_potential_settings() (in module pyrosetta.rosetta.core.init) init_hbond_sp2_correction() (in module pyrosetta.rosetta.core.init) init_kic_loop() (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) init_membrane_center_normal() (pyrosetta.rosetta.core.scoring.MembranePotential method) init_node_info() (in module pyrosetta.rosetta.core.pack.hbonds) init_nonideal_correction() (in module pyrosetta.rosetta.core.init) init_on_new_input() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) init_option() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) init_packing_score_discrim() (in module pyrosetta.rosetta.core.scoring.packstat) init_packing_score_respred() (in module pyrosetta.rosetta.core.scoring.packstat) init_paths() (in module pyrosetta.rosetta.core.init) init_pre_beta_nov15_etable() (in module pyrosetta.rosetta.core.init) init_profiling() (in module pyrosetta.rosetta.core.init) init_random_generators() (in module pyrosetta.rosetta.core.init) init_random_number_generators() (in module pyrosetta.rosetta.core.init) init_resources() (in module pyrosetta.rosetta.core.init) init_restore_score12prime() (in module pyrosetta.rosetta.core.init) init_revert_to_pre_talaris_2013_mistake() (in module pyrosetta.rosetta.core.init) init_revert_to_talaris() (in module pyrosetta.rosetta.core.init) init_rotamers_centroids() (in module pyrosetta.rosetta.protocols.make_rot_lib) init_score_function_corrections() (in module pyrosetta.rosetta.core.init) init_sequence() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) init_shapovalov_lib_fixes_enable_correction() (in module pyrosetta.rosetta.core.init) init_source_revision() (in module pyrosetta.rosetta.core.init) init_spades_score_function_correction() (in module pyrosetta.rosetta.core.init) init_task() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) init_tracers() (in module pyrosetta.rosetta.core.init) init_with_options() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) initialize() (in module pyrosetta.rosetta.basic.options) (pyrosetta.rosetta.core.io.rna.RNA_DataReader method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) initialize_and_check() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) initialize_atomid_map() (in module pyrosetta.rosetta.core.pose) initialize_atomid_map_AtomID() (in module pyrosetta.rosetta.core.pose) initialize_atoms_for_which_we_need_new_dofs() (in module pyrosetta.rosetta.core.pose.rna) initialize_betaresidue_minima() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) initialize_core_id_globals() (in module pyrosetta.rosetta.core.id) initialize_disulfide_bonds() (in module pyrosetta.rosetta.core.pose) initialize_dofs() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) initialize_dun02_aa_parameters() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) initialize_extra_rotamer_flags_from_command_line() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) initialize_extra_rotamer_flags_from_options() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) initialize_filter() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) initialize_for_de_novo_protocol() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) initialize_from() (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) initialize_from_command_line() (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) initialize_from_file() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup method) (pyrosetta.rosetta.protocols.match.Matcher method) initialize_from_file_contents() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup method) initialize_from_file_contents_and_check() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) initialize_from_global_options() (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions method) initialize_from_matcher_task() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) initialize_from_options() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) initialize_from_params() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) initialize_from_residue_type() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) initialize_from_task() (pyrosetta.rosetta.protocols.match.Matcher method) initialize_from_tokens() (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AROMATIC method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.CHARGED method) (pyrosetta.rosetta.core.pack.task.EMPTY method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NC method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.PIKRNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PROPERTY method) (pyrosetta.rosetta.core.pack.task.RESET method) (pyrosetta.rosetta.core.pack.task.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) initialize_ga_randomizer_from_entity_task() (in module pyrosetta.rosetta.protocols.pack_daemon) initialize_graph_for_packing() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) initialize_graph_for_scoring() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) initialize_HBEval_lookup() (in module pyrosetta.rosetta.core.scoring.hbonds)

initialize_hbs() (in module pyrosetta.rosetta.core.pose.ncbb) initialize_input_streams() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) initialize_input_streams_with_residue_info() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) initialize_jump_sampler() (in module pyrosetta.rosetta.protocols.recces.sampler) initialize_native_and_align_pose() (in module pyrosetta.rosetta.core.import_pose) initialize_ncbbs() (in module pyrosetta.rosetta.core.pose.ncbb) initialize_node() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) initialize_o2prime_pack_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.modeler) initialize_oops() (in module pyrosetta.rosetta.core.pose.ncbb) initialize_pack_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.modeler) initialize_parameters() (in module pyrosetta.rosetta.core.pose.full_model_info) initialize_pose_and_other_poses_from_command_line() (in module pyrosetta.rosetta.core.import_pose) initialize_pose_and_other_poses_from_options() (in module pyrosetta.rosetta.core.import_pose) initialize_pose_and_other_poses_from_options_and_input_poses() (in module pyrosetta.rosetta.core.import_pose) initialize_pose_for_rotset_creation() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) initialize_random_chunks() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) initialize_residue_map_from_pose() (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) initialize_residue_type() (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase method) initialize_rna_chunk_library() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) initialize_rnp_aa_rna_backbone() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) initialize_rnp_base_pair() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) initialize_rnp_pair() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) initialize_rnp_pair_dist() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPairDistPotential method) initialize_sample_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.modeler) initialize_sampler() (in module pyrosetta.rosetta.protocols.recces.sampler) initialize_samples() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) initialize_simulation() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.utility.SimulateMPI method) initialize_ss() (in module pyrosetta.rosetta.protocols.comparative_modeling) initialize_stub() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) initialize_sturm() (in module pyrosetta.rosetta.numeric.kinematic_closure) initialize_tag_is_done() (in module pyrosetta.rosetta.core.io.silent) initialize_task_from_entity_resfile_and_secondary_resfile() (in module pyrosetta.rosetta.protocols.pack_daemon) initialize_thermal_sampler() (in module pyrosetta.rosetta.protocols.recces.sampler) initialize_tree_nodes_from_enzcst_io() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) initialize_weights() (pyrosetta.rosetta.protocols.moves.TrialMover method) initialize_xyz_parameters() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body) InitializeByBins (class in pyrosetta.rosetta.protocols.simple_moves.bin_transitions) initialized() (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) InitializeFromOptionCollection (class in pyrosetta.rosetta.core.pack.task.operation) InitializerSentinel (class in pyrosetta.rosetta.ObjexxFCL.internal) inner_job() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) inner_job_nonconst() (pyrosetta.rosetta.protocols.jd2.Job method) InnerJob (class in pyrosetta.rosetta.protocols.jd2) InnerLarvalJob (class in pyrosetta.rosetta.protocols.jd3) inplace_product() (in module pyrosetta.rosetta.numeric) inplace_transpose_product() (in module pyrosetta.rosetta.numeric) inprogress() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) input_domain_map() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) input_etable() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) INPUT_FILE_TYPE (class in pyrosetta.rosetta.protocols.cluster.calibur) input_job_result_indices() (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) input_legrand_sasa_dats() (in module pyrosetta.rosetta.core.scoring.sasa) input_pdb_files_from_command_line() (in module pyrosetta.rosetta.protocols.jd2) input_res() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) input_sasa_dats() (in module pyrosetta.rosetta.core.scoring) (in module pyrosetta.rosetta.core.scoring.packstat.old) input_set() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) input_set_defined() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) input_set_selector() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) input_set_selector_defined() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) input_set_string() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) input_source() (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) input_stub_atom0() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) input_stub_atom0_id() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) input_stub_atom1() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) input_stub_atom1_id() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) input_stub_atom2() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) input_stub_atom2_id() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) input_stub_atom3() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) input_stub_atom3_id() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) input_tag() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) InputStreamWithResidueInfo (class in pyrosetta.rosetta.protocols.stepwise.modeler.protein) insert() (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) insert_aligned_residue() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) insert_aligned_residue_safe() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) insert_atom() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) insert_cdr_into_antibody() (in module pyrosetta.rosetta.protocols.antibody.design) insert_chain_ending() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) insert_chunk_into_pose() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) insert_conformation_by_jump() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) insert_connected_segment() (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) insert_connection_scheme() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) insert_dssp_ss_into_pose() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) insert_edge_ss_into_pose() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) insert_fold_tree_by_jump() (pyrosetta.rosetta.core.kinematics.FoldTree method) insert_fragment() (in module pyrosetta.rosetta.protocols.frags) (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) insert_hit() (pyrosetta.rosetta.protocols.match.HitHasher method) insert_hit_geometry() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) insert_ideal_bonds_at_polymer_junction() (in module pyrosetta.rosetta.core.conformation) insert_ideal_geometry_at_polymer_bond() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) insert_ideal_geometry_at_residue_connection() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) insert_ideal_mainchain_bonds() (in module pyrosetta.rosetta.core.conformation) insert_map() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) insert_match_into_pose() (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) insert_observer() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) insert_or_ignore() (in module pyrosetta.rosetta.basic.database) insert_peptide_edges() (in module pyrosetta.rosetta.protocols.denovo_design) insert_polymer_residue() (pyrosetta.rosetta.core.kinematics.FoldTree method) insert_pose() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) insert_pose_into_pose() (in module pyrosetta.rosetta.protocols.grafting) insert_pose_torsion_override_movemap() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) insert_position() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) insert_random_fragments_in_flexible_protein_regions() (in module pyrosetta.rosetta.protocols.frags) insert_random_protein_chunks() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) insert_residue_by_bond() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) insert_residue_by_chemical_bond() (pyrosetta.rosetta.core.kinematics.FoldTree method) insert_residue_by_jump() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.pose.Pose method) insert_residue_into_atom_tree() (in module pyrosetta.rosetta.core.conformation) insert_sampled_torsion_string_into_taboo_map() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) insert_score_function_method_options_rows() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) insert_size() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) insert_source_residue() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) insert_ss_into_pose() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) insert_ss_into_pose_no_IG_helix() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) insert_target_residue() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) insertion_char() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) insertion_code() (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) insertion_end_residue() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) insertion_length() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) insertion_point_absolute_index() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) insertion_start_residue() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) InsertPoseIntoPoseMover (class in pyrosetta.rosetta.protocols.grafting.simple_movers) InSetExpression (class in pyrosetta.rosetta.protocols.pack_daemon) inside_boundaries() (in module pyrosetta.rosetta.core.membrane) InstallFarnesylMover (class in pyrosetta.rosetta.protocols.farnesyl) instance() (pyrosetta.rosetta.protocols.checkpoint.Timer method) instantiate_any_virtual_sugars() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) instantiate_filter() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) instantiate_mover() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) instantiate_taskoperation() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) instantiate_water_at_octahedral_vertex() (in module pyrosetta.rosetta.protocols.magnesium) instantiated_phosphate() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) int2afteroption() (in module pyrosetta.rosetta.basic.options) int_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) int_to_orientation() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) intafteroption() (in module pyrosetta.rosetta.basic.options) integer() (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) integer_range_restriction() (in module pyrosetta.rosetta.utility.tag) IntegerOption (class in pyrosetta.rosetta.utility.options) IntegerOptionKey (class in pyrosetta.rosetta.utility.options) IntegerVectorOption (class in pyrosetta.rosetta.utility.options) IntegerVectorOptionKey (class in pyrosetta.rosetta.utility.options) integration_test_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) intensity() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) inter() (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) inter_residue_connection_partner() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) InteractingRotamerExplosion (class in pyrosetta.rosetta.protocols.task_operations) InterbondAngleScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) InterchainJumpSelector (class in pyrosetta.rosetta.core.select.jump_selector) InterchainPotential (class in pyrosetta.rosetta.protocols.scoring) interchangeability_group() (pyrosetta.rosetta.core.chemical.ResidueType method) Interface (class in pyrosetta.rosetta.protocols.ligand_docking.ligand_options) interface() (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) interface_builder_ct_namer() (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader method) interface_calc() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) interface_detection_dis() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) interface_distance_cutoff() (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) interface_from_pose() (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) interface_nres() (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) InterfaceAnalyzerMover (class in pyrosetta.rosetta.protocols.analysis) InterfaceBuilderLoader (class in pyrosetta.rosetta.protocols.ligand_docking) InterfaceData (class in pyrosetta.rosetta.protocols.analysis) InterfaceDdGMover (class in pyrosetta.rosetta.protocols.features) InterfaceFeatures (class in pyrosetta.rosetta.protocols.features) InterfaceFeaturesCreator (class in pyrosetta.rosetta.protocols.features) InterfaceInfo (class in pyrosetta.rosetta.protocols.ligand_docking.ligand_options) (class in pyrosetta.rosetta.protocols.scoring) InterfaceInfo.Type (class in pyrosetta.rosetta.protocols.ligand_docking.ligand_options) InterfaceRecapitulationMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) InterfaceRegion (class in pyrosetta.rosetta.protocols.analysis) InterGroupInterfaceByVectorSelector (class in pyrosetta.rosetta.core.select.residue_selector) InterGroupNeighborsCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) InterlockAroma (class in pyrosetta.rosetta.protocols.flxbb) intermediate_structs() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) interp_dspline() (in module pyrosetta.rosetta.core.scoring.electron_density) interp_spline() (in module pyrosetta.rosetta.core.scoring.electron_density) interpolate_2d_func_of_angles() (in module pyrosetta.rosetta.basic) interpolate_bilinear() (in module pyrosetta.rosetta.basic) interpolate_bilinear_by_value() (in module pyrosetta.rosetta.basic) interpolate_get_angle_bins() (in module pyrosetta.rosetta.basic) interpolate_polylinear_by_value() (in module pyrosetta.rosetta.core.pack.dunbrack) interpolate_trilinear() (in module pyrosetta.rosetta.basic) interpolate_trilinear_by_value() (in module pyrosetta.rosetta.basic) interpolate_value_and_deriv() (in module pyrosetta.rosetta.core.scoring) interpolated_analytic_etable_evaluation() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) interpolation_type_enum_to_string() (in module pyrosetta.rosetta.protocols.canonical_sampling) interpolation_type_string_to_enum() (in module pyrosetta.rosetta.protocols.canonical_sampling) InterpolationType (class in pyrosetta.rosetta.protocols.canonical_sampling) intersect() (in module pyrosetta.rosetta.core.membrane) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) intersect_nic() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) intersect_residues() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) intersects() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.protocols.forge.build.Interval method) Interval (class in pyrosetta.rosetta.protocols.forge.build) (class in pyrosetta.rosetta.protocols.jumping) interval() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) interval_to_loop() (in module pyrosetta.rosetta.protocols.forge.methods) intra_elec_scale() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) intra_solv_scale() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) intracomponent_contact() (in module pyrosetta.rosetta.core.pose.symmetry) intrares_upper_atom_neighbors() (pyrosetta.rosetta.core.scoring.NeighborList method) ints_of() (in module pyrosetta.rosetta.ObjexxFCL) inv_virtual_type_for_conf() (in module pyrosetta.rosetta.core.conformation) invalidate() (pyrosetta.rosetta.utility.signals.Link method) invalidate_residues_spanning_cuts() (in module pyrosetta.rosetta.protocols.medal) invDcnst() (pyrosetta.rosetta.core.scoring.RDC_Rohl method) inverse() (in module pyrosetta.rosetta.numeric) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) inverse_rotamers_against_residue() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) inverse_rt6() (in module pyrosetta.rosetta.core.scoring.motif) InverseRotamersRCG (class in pyrosetta.rosetta.protocols.forge.constraints) invert() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) invert_exclude_residues() (in module pyrosetta.rosetta.core.scoring) invert_helix() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) invert_include_residues() (in module pyrosetta.rosetta.protocols.evaluation) InvGeometricFunc (class in pyrosetta.rosetta.protocols.moves) involved_in_phosphate_torsion() (in module pyrosetta.rosetta.core.import_pose) (in module pyrosetta.rosetta.protocols.rna.denovo) InvRotamerDots (class in pyrosetta.rosetta.core.pack.interaction_graph) InvrotCollector (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) invrots() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) InvrotTarget (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) InvrotTree (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) InvrotTreeNodeBase (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) InvrotTreeRCG (class in pyrosetta.rosetta.protocols.forge.constraints) invstub() (in module pyrosetta.rosetta.protocols.sic_dock) inward_normal_to_plane() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) irstream (class in pyrosetta.rosetta.utility.io) is_a_finitenumber() (in module pyrosetta.rosetta.numeric) is_a_submotif() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) is_a_submotif_seed() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) is_aa_name_unknown() (in module pyrosetta.rosetta.core.chemical) is_acceptor() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) is_acetylated_nterminus() (pyrosetta.rosetta.core.chemical.ResidueType method) is_achiral_backbone() (pyrosetta.rosetta.core.chemical.ResidueType method) is_adduct() (pyrosetta.rosetta.core.chemical.ResidueType method) is_alpha_aa() (pyrosetta.rosetta.core.chemical.ResidueType method) is_any_of() (in module pyrosetta.rosetta.ObjexxFCL) is_apolar() (pyrosetta.rosetta.core.conformation.Residue method) is_applicable() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) is_archive_rank() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) is_aromatic() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_atom_axial_or_equatorial_to_ring() (in module pyrosetta.rosetta.core.chemical.rings) (in module pyrosetta.rosetta.core.conformation) (in module pyrosetta.rosetta.core.pose) is_atom_bin_in_range() (in module pyrosetta.rosetta.core.pose.rna) is_attached() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) is_backbone() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) is_base_phosphate_atom_pair() (in module pyrosetta.rosetta.core.chemical.rna) is_base_type() (pyrosetta.rosetta.core.chemical.ResidueType method) is_been_accessed() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) is_being_set() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) is_beta_aa() (pyrosetta.rosetta.core.chemical.ResidueType method) is_beta_aminoacid() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) is_blank() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_blank_seq() (in module pyrosetta.rosetta.core.import_pose) is_blank_string() (in module pyrosetta.rosetta.ObjexxFCL.format) is_bonded() (pyrosetta.rosetta.core.conformation.Residue method) is_bool() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_branch_point() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_bulge() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) is_buried() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) is_camelid() (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) is_cancelled() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) is_canonical() (in module pyrosetta.rosetta.protocols.cyclic_peptide_predict) (pyrosetta.rosetta.core.chemical.ResidueType method) is_canonical_aa() (pyrosetta.rosetta.core.chemical.ResidueType method) is_canonical_beta3_aa() (in module pyrosetta.rosetta.core.chemical) is_canonical_D_aa() (in module pyrosetta.rosetta.core.chemical) is_canonical_L_aa_or_gly() (in module pyrosetta.rosetta.core.chemical) is_canonical_nucleic() (pyrosetta.rosetta.core.chemical.ResidueType method) is_carbohydrate() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_catalytic_seqpos() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) is_centroid() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) is_changed() (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) is_char() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_charged() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_chargedH() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) is_chemical_bond() (pyrosetta.rosetta.core.kinematics.Edge method) is_cl_value() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) is_close_chain_break() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) is_coarse() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_collinear() (in module pyrosetta.rosetta.core.kinematics.tree) is_compatible() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) is_compliant() (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance method) is_conjugatable() (pyrosetta.rosetta.core.chemical.Element method) is_conjugated() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) is_connect() (pyrosetta.rosetta.core.chemical.ICoorAtomID method) is_connected() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) is_conserved() (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) is_continuous() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) is_copy() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) is_counted() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) is_covalent() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) is_cutpoint() (pyrosetta.rosetta.core.kinematics.FoldTree method) is_cutpoint_closed() (in module pyrosetta.rosetta.protocols.stepwise.modeler) is_cutpoint_closed_atom() (in module pyrosetta.rosetta.core.pose.rna) is_cutpoint_closed_torsion() (in module pyrosetta.rosetta.core.pose.rna) is_cutpoint_open() (in module pyrosetta.rosetta.core.pose.rna) is_cyclic() (pyrosetta.rosetta.core.chemical.ResidueType method) is_d_aa() (pyrosetta.rosetta.core.chemical.ResidueType method) is_d_rna() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_designed() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) is_directory() (in module pyrosetta.rosetta.utility.file) is_disulfide() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential method) is_disulfide_bond() (in module pyrosetta.rosetta.core.conformation) is_disulfide_bonded() (pyrosetta.rosetta.core.chemical.ResidueType method) is_DNA() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_donor() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) is_double() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_empty() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) is_end_element() (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) is_equivalent() (pyrosetta.rosetta.core.kinematics.FoldTree method) is_experimental_technique() (pyrosetta.rosetta.core.io.HeaderInformation method) is_extended() (pyrosetta.rosetta.protocols.loops.Loop method) is_fake() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.Bond method) (pyrosetta.rosetta.core.chemical.Element method) is_false_string() (in module pyrosetta.rosetta.utility) is_float() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_flushed() (pyrosetta.logging_support.PythonLoggingSink method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.TracerImpl method) is_foldtype() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) is_freedof() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) is_fullatom() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) is_gamma_aa() (pyrosetta.rosetta.core.chemical.ResidueType method) is_gasteiger_atom_type() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) is_geometry_initialized() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) is_glycosidic_omega2_torsion() (in module pyrosetta.rosetta.core.pose.carbohydrates) is_glycosidic_omega_torsion() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) is_glycosidic_phi_torsion() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) is_glycosidic_psi_torsion() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) is_glycosidic_torsion() (in module pyrosetta.rosetta.core.pose.carbohydrates) is_group() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) is_h2o() (pyrosetta.rosetta.core.chemical.AtomType method) is_H3_rama_kinked() (in module pyrosetta.rosetta.protocols.antibody) is_haro() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomType method) is_heavyatom() (in module pyrosetta.rosetta.core.scoring) (pyrosetta.rosetta.core.chemical.AtomType method) is_het() (pyrosetta.rosetta.core.pose.PDBInfo method) is_hydrogen() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomType method) is_ideal_pose() (in module pyrosetta.rosetta.core.pose) is_ideal_position() (in module pyrosetta.rosetta.core.conformation) (in module pyrosetta.rosetta.core.pose) is_identity() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) is_identity_ignore_gaps() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) is_in_grid() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) is_in_list() (in module pyrosetta.rosetta.protocols.generalized_kinematic_closure) is_in_taboo_map() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) is_inside() (in module pyrosetta.rosetta.protocols.hydrate) is_int() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_interface() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) is_interface_vector() (in module pyrosetta.rosetta.protocols.ligand_docking.ligand_options) is_internal() (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) is_ints() (in module pyrosetta.rosetta.ObjexxFCL) is_inverted_virtual_residue() (pyrosetta.rosetta.core.chemical.ResidueType method) is_jump() (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) is_jump_point() (pyrosetta.rosetta.core.kinematics.FoldTree method) is_known_atom() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) is_l_aa() (pyrosetta.rosetta.core.chemical.ResidueType method) is_l_rna() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_ladder() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) is_legal_greater_than() (in module pyrosetta.rosetta.numeric.kdtree) is_legal_kdtree_below_node() (in module pyrosetta.rosetta.numeric.kdtree) is_legal_less_than() (in module pyrosetta.rosetta.numeric.kdtree) is_ligand() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_ligand_heavyatom() (in module pyrosetta.rosetta.core.scoring) is_ligand_heavyatom_residues() (in module pyrosetta.rosetta.core.scoring) is_lipid() (pyrosetta.rosetta.core.chemical.ResidueType method) is_literal() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) is_long() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_longdouble() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_loop() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) is_loop_residue() (pyrosetta.rosetta.protocols.loops.Loops method) is_lower_cutpoint() (in module pyrosetta.rosetta.core.scoring.methods) is_lower_terminus() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_magnesium() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) is_mainchain_torsion_also_ring_torsion() (in module pyrosetta.rosetta.core.chemical) is_membrane() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) is_membrane_fixed() (in module pyrosetta.rosetta.protocols.membrane) is_membrane_moveable_by_itself() (in module pyrosetta.rosetta.protocols.membrane) is_mergeable() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) is_metal() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.io.NomenclatureManager method) is_metalbinding() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_methylated_cterminus() (pyrosetta.rosetta.core.chemical.ResidueType method) is_mirror_symmetric() (in module pyrosetta.rosetta.core.conformation.symmetry) (in module pyrosetta.rosetta.core.pose.symmetry) is_mixed_mode() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) is_movable() (pyrosetta.rosetta.protocols.nonlocal.Chunk method) is_multi_trial() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) is_multicomponent() (in module pyrosetta.rosetta.core.pose.symmetry) is_NA() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.io.NomenclatureManager method) is_nbr_atom() (in module pyrosetta.rosetta.core.scoring) is_non_peptide_heavy_atom() (in module pyrosetta.rosetta.core.scoring) is_nonempty_input_silent_file() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) is_nonpivot_residue() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) is_normalization_enabled() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) is_num_in_list() (in module pyrosetta.rosetta.protocols.rna.denovo) is_observing() (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.pose.PDBInfo method) is_old_DNA() (pyrosetta.rosetta.core.io.NomenclatureManager method) is_old_RNA() (pyrosetta.rosetta.core.io.NomenclatureManager method) is_oligourea() (pyrosetta.rosetta.core.chemical.ResidueType method) is_on() (pyrosetta.rosetta.protocols.checkpoint.Timer method) is_original_type() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) is_orthogonal() (pyrosetta.rosetta.core.kinematics.Stub method) is_orthonormal() (in module pyrosetta.rosetta.core.scoring.dna) is_pair() (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) is_peptide() (pyrosetta.rosetta.core.kinematics.Edge method) is_peptoid() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_perturbable() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) is_phosphate() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) is_pivot_residue() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) is_PNA() (pyrosetta.rosetta.core.chemical.ResidueType method) is_polar() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_polar_hydrogen() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomType method) is_polymer() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.kinematics.Edge method) is_polymer_bonded() (pyrosetta.rosetta.core.conformation.Residue method) is_polymer_heavyatom() (in module pyrosetta.rosetta.core.scoring) is_polymer_lower() (pyrosetta.rosetta.core.chemical.ICoorAtomID method) is_polymer_upper() (pyrosetta.rosetta.core.chemical.ICoorAtomID method) is_position_conserved_residue() (in module pyrosetta.rosetta.core.pose) is_protected() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) is_protein() (in module pyrosetta.rosetta.protocols.stepwise.modeler) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_protein_backbone() (in module pyrosetta.rosetta.core.scoring) is_protein_backbone_including_O() (in module pyrosetta.rosetta.core.scoring) is_protein_CA() (in module pyrosetta.rosetta.core.scoring) is_protein_CA_or_CB() (in module pyrosetta.rosetta.core.scoring) is_protein_CA_or_equiv() (in module pyrosetta.rosetta.core.scoring) is_protein_sidechain_heavyatom() (in module pyrosetta.rosetta.core.scoring) is_proton() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) is_proton_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) is_pseudo_bonded() (pyrosetta.rosetta.core.conformation.Residue method) is_purine() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_pyrimidine() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_qsar_map_attached() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) is_referencepose_number() (in module pyrosetta.rosetta.core.pose) is_relevant() (pyrosetta.rosetta.utility.options.OptionCollection method) is_repulsive() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_required() (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) is_res_exposed() (in module pyrosetta.rosetta.core.scoring.sasa) is_residues_in_contact() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) is_ring_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) is_RNA() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_RNA_base() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) is_RNA_base_atom() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) is_rna_chainbreak() (in module pyrosetta.rosetta.core.pose.rna) is_root() (pyrosetta.rosetta.core.kinematics.FoldTree method) is_rot_sample_name() (in module pyrosetta.rosetta.core.pack.task) is_same_sugar_pucker() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) is_scatom() (in module pyrosetta.rosetta.core.scoring) is_scofx_cstfied() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) is_set_s_kk() (pyrosetta.rosetta.protocols.cluster.DataPoint method) is_short() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_sidechain_amine() (pyrosetta.rosetta.core.chemical.ResidueType method) is_sidechain_thiol() (pyrosetta.rosetta.core.chemical.ResidueType method) is_similar_aa() (pyrosetta.rosetta.core.conformation.Residue method) is_similar_rotamer() (pyrosetta.rosetta.core.conformation.Residue method) is_simple_tree() (pyrosetta.rosetta.core.kinematics.FoldTree method) is_singlecomponent() (in module pyrosetta.rosetta.core.pose.symmetry) is_solution_trivial() (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) is_solvent() (pyrosetta.rosetta.core.chemical.ResidueType method) is_sp2_proton_chi() (in module pyrosetta.rosetta.core.chemical) is_sparis_foldtype() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) is_sri() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_string() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_string_numeric() (in module pyrosetta.rosetta.utility) is_sugar() (pyrosetta.rosetta.core.io.NomenclatureManager method) is_sugar_virtual() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) is_surface() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_symmetric() (in module pyrosetta.rosetta.core.conformation.symmetry) (in module pyrosetta.rosetta.core.pose.symmetry) is_symmetric_partner_of() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) is_terminal() (pyrosetta.rosetta.protocols.loops.Loop method) is_terminus() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_this_strand_at_edge() (in module pyrosetta.rosetta.protocols.features.strand_assembly) is_this_strand_at_edge_by_looking_db() (in module pyrosetta.rosetta.protocols.features.strand_assembly) is_TNA() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_tna_chainbreak() (in module pyrosetta.rosetta.core.pose.rna) is_torsion_valid() (in module pyrosetta.rosetta.core.pose.rna) is_triazolemer() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_true_string() (in module pyrosetta.rosetta.utility) is_type() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_uint() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_ulong() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_undefined() (in module pyrosetta.rosetta.utility) is_upper_cutpoint() (in module pyrosetta.rosetta.core.scoring.methods) is_upper_terminus() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_ushort() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_using() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) is_valid() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) is_valid_chunk() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) is_valid_modification_affix() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) is_valid_quota_pool_name() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) is_valid_record_type() (pyrosetta.rosetta.core.io.pdb.RecordCollection method) is_valid_ring_affix() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) is_valid_sugar_code() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) is_value() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) is_variant_type() (pyrosetta.rosetta.core.chemical.ResidueProperties method) is_virtual() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) (pyrosetta.rosetta.core.conformation.Residue method) is_virtual_base() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) is_virtual_residue() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_water() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) IsBondInRing() (pyrosetta.rosetta.core.chemical.Bond method) IsBondOrderKnown() (pyrosetta.rosetta.core.chemical.Bond method) isClose() (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.PCluster method) isCompound() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) isDigit() (in module pyrosetta.rosetta.protocols.sparta) isDirExists() (in module pyrosetta.rosetta.protocols.sparta) isEmpty() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) isGenericRB() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) isHelix() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) isinf() (in module pyrosetta.rosetta.utility) isnan() (in module pyrosetta.rosetta.utility) isometry() (pyrosetta.rosetta.core.chemical.Bond method) isPowerOfTwo() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) isSheet() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) isSimple() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) isSolventExposed() (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.PCluster method) isSpace() (in module pyrosetta.rosetta.protocols.sparta) isTarget() (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.PCluster method) isTooSmall() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) iterate_tensor_weights() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) IteratedConvergenceMover (class in pyrosetta.rosetta.protocols.moves) iteration() (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) iterations() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) itime() (in module pyrosetta.rosetta.ObjexxFCL) itoa() (in module pyrosetta.rosetta.protocols.sparta) itterative() (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) ivalue() (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) izstream (class in pyrosetta.rosetta.utility.io)

J

j() (pyrosetta.rosetta.core.pose.rna.BasePairStep method) j_next() (pyrosetta.rosetta.core.pose.rna.BasePairStep method) Jcomputed() (pyrosetta.rosetta.core.scoring.RDC method) JCoupling (class in pyrosetta.rosetta.protocols.frag_picker.scores) jd2_used() (in module pyrosetta.rosetta.protocols.jd2) jd_output_suffix() (pyrosetta.rosetta.protocols.jd3.output.OutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification method) Jdipolar() (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) Job (class in pyrosetta.rosetta.protocols.jd2) (class in pyrosetta.rosetta.protocols.jd3) job_available_on_command_line() (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputter method) job_def_complex_type_name() (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) job_definition_xsd() (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) job_failed() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) job_has_already_completed() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter method) job_has_completed() (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) job_id() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) job_index() (pyrosetta.rosetta.protocols.jd3.LarvalJob method) job_inputter() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) job_inputter_input_source() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) job_inputter_input_source_to_string() (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) job_outputter() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) job_results_that_should_be_discarded() (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) job_succeeded() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) job_tag() (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) job_tag_with_index_suffix() (pyrosetta.rosetta.protocols.jd3.LarvalJob method) JobDataFeaturesCreator (class in pyrosetta.rosetta.protocols.features) jobdef_tag() (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) jobindex_on_originating_node() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) JobInputter (class in pyrosetta.rosetta.protocols.jd2) JobInputterCreator (class in pyrosetta.rosetta.protocols.jd2) JobOutputIndex (class in pyrosetta.rosetta.protocols.jd3)

JobOutputter (class in pyrosetta.rosetta.protocols.jd2) JobOutputterCreator (class in pyrosetta.rosetta.protocols.jd2) JobQueen (class in pyrosetta.rosetta.protocols.jd3) JobResult (class in pyrosetta.rosetta.protocols.jd3) jobs_that_should_be_output() (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) JobsContainer (class in pyrosetta.rosetta.protocols.jd2) JobStatus (class in pyrosetta.rosetta.protocols.jd3) JobSummary (class in pyrosetta.rosetta.protocols.jd3) join() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) JointScore (class in pyrosetta.rosetta.protocols.sic_dock) JScoreEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) JsonEmitter (class in pyrosetta.rosetta.basic) judge_facing() (in module pyrosetta.rosetta.protocols.features.strand_assembly) Jump (class in pyrosetta.rosetta.core.kinematics) jump() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.import_pose.libraries.RNA_PairingTemplate method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) jump_atom_id() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) jump_backward() (pyrosetta.rosetta.core.import_pose.libraries.RNA_PairingTemplate method) jump_distance() (in module pyrosetta.rosetta.core.kinematics) jump_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) jump_exists() (pyrosetta.rosetta.core.kinematics.FoldTree method) jump_forward() (pyrosetta.rosetta.core.import_pose.libraries.RNA_PairingTemplate method) jump_id() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) jump_id_begin() (pyrosetta.rosetta.core.kinematics.MoveMap method) jump_id_end() (pyrosetta.rosetta.core.kinematics.MoveMap method) jump_nr() (pyrosetta.rosetta.core.kinematics.FoldTree method) jump_num() (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) jump_num_sym_dof() (in module pyrosetta.rosetta.core.pose.symmetry) jump_pairs() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) jump_point() (pyrosetta.rosetta.core.kinematics.FoldTree method) jump_res_map() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) jump_selector_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader method) jump_which_partitions() (in module pyrosetta.rosetta.core.kinematics) JumpAtom (class in pyrosetta.rosetta.core.kinematics.tree) jumpAtoms() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) jumpAtoms_defined() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) JumpDownstreamSelector (class in pyrosetta.rosetta.core.select.residue_selector) JumpID (class in pyrosetta.rosetta.core.id) JumpIndexSelector (class in pyrosetta.rosetta.core.select.jump_selector) JumpingFrame (class in pyrosetta.rosetta.core.fragment) JumpNrEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) JumpRotamerSidechainMover (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) jumps_and_cuts_from_pose() (in module pyrosetta.rosetta.protocols.forge.methods) jumps_connected_to_position() (in module pyrosetta.rosetta.protocols.forge.methods) jumps_from_pose() (in module pyrosetta.rosetta.core.pose) JumpSelector (class in pyrosetta.rosetta.protocols.jumping) JumpSelectorLoader (class in pyrosetta.rosetta.protocols.parser) JumpSetup (class in pyrosetta.rosetta.protocols.jumping) JumpsFromAllPairings (class in pyrosetta.rosetta.protocols.jumping) JumpUpstreamSelector (class in pyrosetta.rosetta.core.select.residue_selector) just_modeling_RNA() (in module pyrosetta.rosetta.core.import_pose) (in module pyrosetta.rosetta.core.pose) just_protein() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) just_rna() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) just_smooth_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method)

K

k() (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering method) k_angle() (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) k_length() (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) k_medoids_on_the_fly() (in module pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster) k_medoids_with_edge_precalculation() (in module pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster) k_torsion() (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) k_torsion_improper() (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) k_torsion_proton() (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) KarplusFunc (class in pyrosetta.rosetta.core.scoring.func) KCluster (class in pyrosetta.rosetta.protocols.toolbox) KClusterData (class in pyrosetta.rosetta.protocols.toolbox) KClusterElement (class in pyrosetta.rosetta.protocols.toolbox) KDPointList (class in pyrosetta.rosetta.numeric.kdtree) keep_1st_child_pos() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) keep_aas() (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) keep_all_protocol() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) keep_checkpoint_file() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) keep_current() (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) keep_dof_fixed() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) keep_filters() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) keep_fragments() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) keep_input_protonation_state() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) keep_known_bb_torsions_at_junctions() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) keep_native() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) keep_stats_type() (pyrosetta.rosetta.protocols.moves.TrialMover method) keep_stub_in_residue() (pyrosetta.rosetta.core.kinematics.Edge method) keep_task_allowed_aas() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) KeepRegionMover (class in pyrosetta.rosetta.protocols.grafting.simple_movers) Key (class in pyrosetta.rosetta.utility.keys) key() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) keyname() (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.SilentStructCreator method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator method) (pyrosetta.rosetta.core.sequence.SequenceCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.filters.FilterCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMoverCreator method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraintCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraintCreator method) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator method) (pyrosetta.rosetta.protocols.moves.MoverCreator method) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator method) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation method)

keyword_in_progress() (pyrosetta.rosetta.core.io.HeaderInformation method) keywords() (pyrosetta.rosetta.core.io.HeaderInformation method) kf_cexp() (in module pyrosetta.rosetta.numeric.fourier) kic_close_loops_in_samples() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close) kic_modeler_if_relevant() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) kic_sampling() (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) KicMover (class in pyrosetta.rosetta.protocols.kinematic_closure) kill_antiparallel() (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) kill_parallel() (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) KinematicMover (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) KinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) kinematics() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) KinematicWrapper (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) kink_anion_atoms() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) kink_anion_residue() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) kink_bb_Hbond() (in module pyrosetta.rosetta.protocols.antibody) kink_begin() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) kink_cation_atoms() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) kink_cation_residue() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) kink_constrain_antibody_H3() (in module pyrosetta.rosetta.protocols.antibody) kink_dihedral() (in module pyrosetta.rosetta.protocols.antibody) kink_end() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) kink_RD_Hbond() (in module pyrosetta.rosetta.protocols.antibody) kink_trp() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) kink_Trp_Hbond() (in module pyrosetta.rosetta.protocols.antibody) kinmover() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) kiss_dct() (in module pyrosetta.rosetta.numeric.fourier) kiss_dct_state (class in pyrosetta.rosetta.numeric.fourier) kiss_fft() (in module pyrosetta.rosetta.numeric.fourier) kiss_fft_cleanup() (in module pyrosetta.rosetta.numeric.fourier) kiss_fft_next_fast_size() (in module pyrosetta.rosetta.numeric.fourier) kiss_fft_split() (in module pyrosetta.rosetta.numeric.fourier) kiss_fft_stride() (in module pyrosetta.rosetta.numeric.fourier) kiss_fftnd() (in module pyrosetta.rosetta.numeric.fourier) kiss_fftnd_state (class in pyrosetta.rosetta.numeric.fourier) kiss_fftndr() (in module pyrosetta.rosetta.numeric.fourier) kiss_fftndr_state (class in pyrosetta.rosetta.numeric.fourier) kiss_fftndri() (in module pyrosetta.rosetta.numeric.fourier) kiss_fftr() (in module pyrosetta.rosetta.numeric.fourier) kiss_fftr_next_fast_size_real() (in module pyrosetta.rosetta.numeric.fourier) kiss_fftr_state (class in pyrosetta.rosetta.numeric.fourier) kiss_fftri() (in module pyrosetta.rosetta.numeric.fourier) kiss_fftsplit_state (class in pyrosetta.rosetta.numeric.fourier) kiss_idct() (in module pyrosetta.rosetta.numeric.fourier) kl_divergence() (in module pyrosetta.rosetta.numeric.statistics) KMedoid (class in pyrosetta.rosetta.protocols.toolbox) KMGT() (in module pyrosetta.rosetta.protocols.sic_dock) KofNConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) KromerMann (class in pyrosetta.rosetta.core.scoring.electron_density) (class in pyrosetta.rosetta.core.scoring.fiber_diffraction) KRSQueryType (class in pyrosetta.rosetta.protocols.kinmatch)

L

L() (in module pyrosetta.rosetta.ObjexxFCL.format) l() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) L1_pattern() (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager method) l1_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) l2_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) L3_pattern() (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager method) l3_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) l_initialized() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) l_no_notify() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) label() (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) label_atom() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) label_atom_name() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) label_atom_type() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) label_resonance() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) label_resonance_id() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) label_tolerance() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) LabelPoseFromResidueSelectorMover (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) LabelResonance (class in pyrosetta.rosetta.protocols.noesy_assign) lambda_memory() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) LAMBEGO_Similarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) landing_domain() (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) landing_pos() (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) LargeNstructJobInputter (class in pyrosetta.rosetta.protocols.jd2) largest_continuous_atom_map() (in module pyrosetta.rosetta.protocols.legacy_sewing) largestTargetPocketVolume() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) larval_job_needed_for_completed_job_summary() (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) larval_job_needed_for_note_job_completed() (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) LarvalJob (class in pyrosetta.rosetta.protocols.jd3) last() (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) last_accept() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) last_accepted() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) last_accepted_pose() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) last_accepted_score() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) last_accepted_scores() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) last_angle() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) last_backbone_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) last_batch_id() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) last_controlling_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) last_end_atom_name() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) last_ind_assigned() (pyrosetta.rosetta.protocols.mean_field.ResHashMap method) last_index() (in module pyrosetta.rosetta.ObjexxFCL) last_inner_score_delta_over_temperature() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) last_key() (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) last_move() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) last_move_succeeded() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) last_mutation() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) last_nchi() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) last_proposal_density_ratio() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) last_received_from() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) last_residue() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) last_residue_index() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) last_score() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) last_section() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) last_segment_id() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) last_slide_good() (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) last_start_atom_name() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) last_symmetry_mirror() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) last_symmetry_repeats() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) last_tested_scores() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) last_uniform() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) last_withinrot() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) launch_atom() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) LayerSelector (class in pyrosetta.rosetta.core.select.residue_selector) lazy_ig() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) lb() (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) LeapIndex (class in pyrosetta.rosetta.protocols.loophash) leave_as_is() (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) left_justified() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) left_justify() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) left_string_of() (in module pyrosetta.rosetta.ObjexxFCL) left_stub_atoms() (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) legacy_global_requirements_ct_namer() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory method) legacy_global_requirements_group_name() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory method) legacy_intra_segment_requirements_ct_namer() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory method) legacy_intra_segment_requirements_group_name() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory method) LegacyAssemblyConstraintsMover (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyGlobalRequirementCreator (class in pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements) LegacyKicSampler (class in pyrosetta.rosetta.protocols.loop_modeling.samplers) LegacyReadNativeRotamersFile (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyReadRepeatNativeRotamersFile (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyRequirementFactory (class in pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements) legal() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) legal_check() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) legal_default() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) legal_default_check() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) legal_default_report() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) legal_default_size() (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) legal_default_value() (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method)

legal_limits_report() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) legal_report() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) legal_size() (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) legal_size_report() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) legal_specs_report() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) legal_string() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) legal_value() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) LeGrandSasa (class in pyrosetta.rosetta.core.scoring.sasa) len() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) len_trim() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) len_trim_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) length() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) (pyrosetta.rosetta.protocols.forge.build.Interval method) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.nonlocal.Chunk method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) length_normalized_distance() (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) length_type() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) LengthEvent (class in pyrosetta.rosetta.core.conformation.signals) LengthEvent.Tag (class in pyrosetta.rosetta.core.conformation.signals) LengthEventCollector (class in pyrosetta.rosetta.core.pose.datacache) LengthGen (class in pyrosetta.rosetta.core.fragment.picking_old.vall.gen) lengths_shifts() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) let_rigid_body_jumps_move() (in module pyrosetta.rosetta.protocols.rna.denovo) level_2_grid_coord() (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) lge() (in module pyrosetta.rosetta.ObjexxFCL) lgt() (in module pyrosetta.rosetta.ObjexxFCL) lib_full_path() (in module pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks) library() (pyrosetta.rosetta.protocols.frags.FragLib method) library_name() (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) library_size() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) LigandBaseProtocol (class in pyrosetta.rosetta.protocols.ligand_docking) LigandMetalContactSelector (class in pyrosetta.rosetta.protocols.residue_selectors) light_chain_type_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) light_chain_type_is_present() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) light_chain_type_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) light_framework() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) LightChainTypeEnum (class in pyrosetta.rosetta.protocols.antibody) limit() (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) limit_chunk_size() (in module pyrosetta.rosetta.protocols.nonlocal) limit_rotamer_set() (in module pyrosetta.rosetta.protocols.multistate_design) limit_to_positions() (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) limit_waters() (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) LimitAromaChi2Operation (class in pyrosetta.rosetta.protocols.task_operations) Line (class in pyrosetta.rosetta.core.sequence) linear_chainbreak() (in module pyrosetta.rosetta.protocols.denovo_design) (in module pyrosetta.rosetta.protocols.forge.methods) linear_interpolate() (in module pyrosetta.rosetta.core.scoring.constraints) LinearBranchEnergy (class in pyrosetta.rosetta.core.scoring.methods) LinearChainbreakEnergy (class in pyrosetta.rosetta.core.scoring.methods) linearize_fold_tree() (in module pyrosetta.rosetta.core.kinematics) LineMinimizationAlgorithm (class in pyrosetta.rosetta.core.optimization) linenum() (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) Link (class in pyrosetta.rosetta.utility.signals) link_in_vector() (in module pyrosetta.rosetta.core.io) link_map() (pyrosetta.rosetta.core.io.StructFileRep method) link_torsion_vectors() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) link_vertex_to_generators() (in module pyrosetta.rosetta.core.scoring.power_diagram) LinkageConformerData (class in pyrosetta.rosetta.core.chemical.carbohydrates) LinkageConformerMover (class in pyrosetta.rosetta.protocols.carbohydrates) linker_count2score() (in module pyrosetta.rosetta.protocols.sic_dock) linker_name() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) linkExemplarsThroughSolvent() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) LinkInformation (class in pyrosetta.rosetta.core.io) LinkResidues (class in pyrosetta.rosetta.protocols.task_operations) LinkUnit (class in pyrosetta.rosetta.utility.signals) linmem_ig() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) linmem_ig_history_size() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) lipid_acc_data() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) lipid_burial() (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo method) lipid_exposure() (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo method) LipidAccInfo (class in pyrosetta.rosetta.core.conformation.membrane) lipsfile() (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) list_amino_acid_options() (in module pyrosetta.rosetta.protocols.multistate_design) list_dir() (in module pyrosetta.rosetta.utility.file) list_pools() (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) listener_tag_to_name() (in module pyrosetta.rosetta.basic.mpi) listener_tags (class in pyrosetta.rosetta.basic.mpi) literal_value() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) live() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) lj_cutoff() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) lj_radius() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.MMAtomType method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lj_radius_sq() (pyrosetta.rosetta.core.chemical.MMAtomType method) lj_slope_intercept() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lj_switch_dis2sigma() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lj_three_bond_radius() (pyrosetta.rosetta.core.chemical.MMAtomType method) lj_three_bond_radius_sq() (pyrosetta.rosetta.core.chemical.MMAtomType method) lj_three_bond_wdepth() (pyrosetta.rosetta.core.chemical.MMAtomType method) lj_use_hbond_radii() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lj_use_lj_deriv_slope() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lj_use_water_radii() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lj_water_dis() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lj_water_hdis() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lj_wdepth() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.MMAtomType method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) ljatr() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) ljrep() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) ljust() (in module pyrosetta.rosetta.ObjexxFCL) lk_dgfree() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lk_dgrefce() (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lk_inv_lambda2() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lk_lambda() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lk_min_dis2sigma() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lk_volume() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lkb_pwat() (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) lkb_pwat_rotamers_setup() (in module pyrosetta.rosetta.core.pack) LKB_ResiduesInfo (class in pyrosetta.rosetta.core.scoring.lkball) LKBallDatabase (class in pyrosetta.rosetta.core.scoring.lkball) lle() (in module pyrosetta.rosetta.ObjexxFCL) llt() (in module pyrosetta.rosetta.ObjexxFCL) lm_enorm() (in module pyrosetta.rosetta.numeric.nls) lm_printout_std() (in module pyrosetta.rosetta.numeric.nls) load() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.utility.options.OptionCollection method) load_bin_params() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) load_binary() (pyrosetta.rosetta.protocols.cluster.APCluster method) load_build_position_data() (in module pyrosetta.rosetta.protocols.motifs) load_cdr_design_data() (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) load_cdr_design_data_for_cdrs() (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) load_cdr_pose() (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) load_checkpoint() (in module pyrosetta.rosetta.protocols.dna) load_checkpoint_file() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) load_component_weights() (in module pyrosetta.rosetta.protocols.optimize_weights) load_data() (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader method) (pyrosetta.rosetta.protocols.parser.DataLoader method) (pyrosetta.rosetta.protocols.parser.DatabaseSessionLoader method) (pyrosetta.rosetta.protocols.parser.FragSetLoader method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) (pyrosetta.rosetta.protocols.parser.ResLvlTaskOperationLoader method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader method) (pyrosetta.rosetta.protocols.parser.SimpleMetricLoader method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) load_decoys() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) load_dist_table() (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance method) load_dna_design_defs_from_file() (in module pyrosetta.rosetta.protocols.dna) load_dna_design_defs_from_options() (in module pyrosetta.rosetta.protocols.dna) load_dna_design_defs_from_strings() (in module pyrosetta.rosetta.protocols.dna) load_fastsax_spectrum() (in module pyrosetta.rosetta.core.scoring.saxs) load_ff() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) load_ff_from_db() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) load_form_factors() (in module pyrosetta.rosetta.core.scoring.saxs) load_from_rcsb() (in module pyrosetta.toolbox.rcsb) load_into_pose() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) load_loop_definitions() (in module pyrosetta.rosetta.protocols.loops.loops_definers) load_native_pose_as_reference() (pyrosetta.rosetta.protocols.analysis.simple_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.TotalEnergyMetric method) load_options_from_file() (pyrosetta.rosetta.utility.options.OptionCollection method) load_options_from_file_exception() (pyrosetta.rosetta.utility.options.OptionCollection method) load_options_from_option_system() (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) load_options_from_stream() (pyrosetta.rosetta.utility.options.OptionCollection method) load_pdb_id_from_file() (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) load_poses() (in module pyrosetta.rosetta.protocols.simple_filters) load_s_and_l() (in module pyrosetta.rosetta.protocols.jobdist) (in module pyrosetta.rosetta.protocols.stepwise.setup) load_silent_file() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) load_silent_files() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) load_templates_from_pdbs() (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) load_trial_number_from_checkpoint() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) load_unboundrot() (in module pyrosetta.rosetta.core.pack.dunbrack) loader_map() (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory method) loader_name() (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader method) (pyrosetta.rosetta.protocols.parser.DatabaseSessionLoader method) (pyrosetta.rosetta.protocols.parser.FragSetLoader method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) (pyrosetta.rosetta.protocols.parser.ResLvlTaskOperationLoader method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader method) (pyrosetta.rosetta.protocols.parser.SimpleMetricLoader method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) loader_type() (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator method) (pyrosetta.rosetta.core.fragment.FragmentSetLoaderCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator method) LoadUnboundRotMover (class in pyrosetta.rosetta.protocols.simple_moves) LoadVarSolDistSasaCalculatorMover (class in pyrosetta.rosetta.protocols.vardist_solaccess) local2global() (pyrosetta.rosetta.core.kinematics.Stub method) local_coord_matrix() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) local_name() (pyrosetta.rosetta.utility.file.FileName method) local_rotamer_id() (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) LocalBackboneMover (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover) LocalCoordinateConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) LocalInserter (class in pyrosetta.rosetta.protocols.loophash) LocalInserter_SimpleMin (class in pyrosetta.rosetta.protocols.loophash) locate_resource_stream() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) locate_rosetta_database() (in module pyrosetta.rosetta.core.init) location_in_parent_node() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) locator_map() (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) locator_tag() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) locator_type() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator method) log() (in module pyrosetta.rosetta.numeric) log_angles() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) log_lengths() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) log_torsions() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) logarithm() (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) logdgaussian() (in module pyrosetta.rosetta.core.scoring.constraints) logdgaussian_deriv() (in module pyrosetta.rosetta.core.scoring.constraints) LogFilePerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) LogicalSelector (class in pyrosetta.rosetta.protocols.pose_selectors) long_mutate_strategy() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) long_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) long_range_container() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) long_range_damping_length() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) long_range_energies_begin() (pyrosetta.rosetta.core.scoring.ScoreFunction method) long_range_energies_end() (pyrosetta.rosetta.core.scoring.ScoreFunction method) long_range_type() (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) long_string_rep() (pyrosetta.rosetta.protocols.contact_map.Contact method) LongAxisRotationFreePeptideMover (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers) longdouble_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) LongestContinuousApolarSegmentFilter (class in pyrosetta.rosetta.protocols.simple_filters) LongestContinuousPolarSegmentFilter (class in pyrosetta.rosetta.protocols.simple_filters) LongRangeEnergyType (class in pyrosetta.rosetta.core.scoring.methods) look_for_dna() (in module pyrosetta.rosetta.core.import_pose) look_for_jumps() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) look_for_jumps_to_next() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) look_for_jumps_to_previous() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) look_for_non_jump_reference_to_next() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) look_for_non_jump_reference_to_previous() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) look_for_unique_jump_to_moving_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) lookup() (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) lookup_angle() (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) lookup_angle_legacy() (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) lookup_cp_map() (in module pyrosetta.rosetta.core.scoring.trie) lookup_idx() (in module pyrosetta.rosetta.core.scoring.rna.data) lookup_improper() (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) lookup_length() (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) lookup_length_legacy() (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) lookup_stored_constraints() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) lookup_three_bond() (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) lookup_torsion_legacy() (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) lookup_withkey() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) LookupMode (class in pyrosetta.rosetta.protocols.indexed_structure_store.filters) Loop (class in pyrosetta.rosetta.core.scoring.loop_graph) (class in pyrosetta.rosetta.protocols.fldsgn.topology) (class in pyrosetta.rosetta.protocols.loops) loop() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) loop_ang() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) loop_begin() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) loop_centroid_relax() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) loop_close_use_6D_potential() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) loop_cut() (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) loop_def_loader_ct_namer() (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader method) loop_definer_xml_schema_group_name() (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) loop_dih() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) loop_end() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) loop_fa_relax() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) loop_file_name() (pyrosetta.rosetta.protocols.loops.Loops method) loop_fraction() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) loop_frags() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) loop_id() (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) loop_incident() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) loop_index_of_residue() (pyrosetta.rosetta.protocols.loops.Loops method) loop_info() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) loop_local_rmsd() (in module pyrosetta.rosetta.protocols.loops) Loop_lt (class in pyrosetta.rosetta.protocols.loops) loop_model() (pyrosetta.rosetta.protocols.LoopRebuild method) loop_mover_fold_tree_constant() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) loop_mover_from_tag() (in module pyrosetta.rosetta.protocols.loop_modeling.utilities) loop_mover_str() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) loop_of_residue() (pyrosetta.rosetta.protocols.loops.Loops method) loop_protocol_attlist() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) loop_rmsd() (in module pyrosetta.rosetta.protocols.loops) loop_rmsd_with_superimpose() (in module pyrosetta.rosetta.protocols.loops) loop_rmsd_with_superimpose_core() (in module pyrosetta.rosetta.protocols.loops) loop_seqid_threshold() (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) loop_seqid_thresholds() (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) loop_size() (pyrosetta.rosetta.protocols.loops.Loops method) loop_sizes() (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) loop_start() (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) loop_start_without_overlap() (in module pyrosetta.rosetta.protocols.denovo_design) loop_stop_without_overlap() (in module pyrosetta.rosetta.protocols.denovo_design) LoopAnalyzerFilter (class in pyrosetta.rosetta.protocols.loops.filters) LoopAnchorFeaturesCreator (class in pyrosetta.rosetta.protocols.features) LoopBuild_main() (in module pyrosetta.rosetta.protocols.loop_build) LoopBuilder (class in pyrosetta.rosetta.protocols.loop_modeling) LoopConfiguration (class in pyrosetta.rosetta.protocols.loops) LoopFilter (class in pyrosetta.rosetta.protocols.loop_modeling.utilities) loopfinder() (in module pyrosetta.rosetta.protocols.loops) loophash_cycles() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) loophash_main() (in module pyrosetta.rosetta.protocols.loophash) LoopHashDiversifier (class in pyrosetta.rosetta.protocols.loophash) LoopHashLibraryLoader (class in pyrosetta.rosetta.protocols.loophash) LoopHashLibraryLoaderCreator (class in pyrosetta.rosetta.protocols.loophash) LoopHashMap (class in pyrosetta.rosetta.protocols.loophash) LoopHashMoverWrapper (class in pyrosetta.rosetta.protocols.loophash) LoopHashPerturber (class in pyrosetta.rosetta.protocols.loop_modeler.perturbers) LoopHashRelaxProtocol (class in pyrosetta.rosetta.protocols.loophash) LoopHashSampler (class in pyrosetta.rosetta.protocols.loophash) LoopLengthChange (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) LoopModeler (class in pyrosetta.rosetta.protocols.loop_modeler) LoopMover (class in pyrosetta.rosetta.protocols.loop_modeling) (class in pyrosetta.rosetta.protocols.loops.loop_mover) LoopMover_Perturb_CCD (class in pyrosetta.rosetta.protocols.loops.loop_mover.perturb) LoopMover_Perturb_CCDCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.perturb) LoopMover_Perturb_KICCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.perturb) LoopMover_Perturb_QuickCCD (class in pyrosetta.rosetta.protocols.loops.loop_mover.perturb) LoopMover_Perturb_QuickCCD_Moves (class in pyrosetta.rosetta.protocols.loops.loop_mover.perturb) LoopMover_Perturb_QuickCCD_MovesCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.perturb) LoopMover_Perturb_QuickCCDCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.perturb) LoopMover_Refine_BackrubCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) LoopMover_Refine_CCDCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) LoopMover_Refine_KICCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) LoopMover_SlidingWindow (class in pyrosetta.rosetta.protocols.loop_build) LoopMover_SlidingWindowCreator (class in pyrosetta.rosetta.protocols.loop_build) LoopMoverFactory (class in pyrosetta.rosetta.protocols.loops) LoopMoverGroup (class in pyrosetta.rosetta.protocols.loop_modeling.utilities) LoopOver (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) LoopPivots (class in pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers) LoopProtocol (class in pyrosetta.rosetta.protocols.loop_modeling) LoopRebuild (class in pyrosetta.rosetta.protocols) LoopRefine (class in pyrosetta.rosetta.protocols) LoopRefineInnerCycleContainerCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) LoopRefineInnerCycleFactory (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) LoopRefineInnerCycleName (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) loopres_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) loopres_base2_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) loopres_base_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) LoopResult (class in pyrosetta.rosetta.protocols.loops.loop_mover) LoopRlxMover (class in pyrosetta.rosetta.protocols.antibody_legacy) Loops (class in pyrosetta.rosetta.protocols.loops) loops() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) loops_are_closed() (in module pyrosetta.rosetta.protocols.comparative_modeling) loops_around_residues() (in module pyrosetta.rosetta.protocols.loops) loops_file_data() (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) loops_from_alignment() (in module pyrosetta.rosetta.protocols.comparative_modeling) loops_from_string() (in module pyrosetta.rosetta.protocols.loops) loops_from_transitive_alignments() (in module pyrosetta.rosetta.protocols.comparative_modeling) loops_set_chainbreak_weight() (in module pyrosetta.rosetta.protocols.loops.loop_mover) loops_set_move_map() (in module pyrosetta.rosetta.protocols.loops) LoopsDatabaseDefiner (class in pyrosetta.rosetta.protocols.loops.loops_definers) LoopsDatabaseDefinerCreator (class in pyrosetta.rosetta.protocols.loops.loops_definers) LoopsDefinerCreator (class in pyrosetta.rosetta.protocols.loops.loops_definers) LoopsDefinerFactory (class in pyrosetta.rosetta.protocols.loops.loops_definers) LoopsDefinerLoader (class in pyrosetta.rosetta.protocols.loops.loops_definers) LoopsExplicitDefinerCreator (class in pyrosetta.rosetta.protocols.loops.loops_definers) LoopsFileDefinerCreator (class in pyrosetta.rosetta.protocols.loops.loops_definers) LoopsFileIO (class in pyrosetta.rosetta.protocols.loops) LoopsFileLoader (class in pyrosetta.rosetta.protocols.loops) LoopsFileLoaderCreator (class in pyrosetta.rosetta.protocols.loops) loopstring_to_loopregions() (in module pyrosetta.rosetta.protocols.mpi_refinement) loopstring_to_loopvector() (in module pyrosetta.rosetta.protocols.mpi_refinement) lores() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) low_res() (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) low_temp() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) lower() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) lower_chain() (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) lower_connect() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) lower_connect_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) lower_connect_id() (pyrosetta.rosetta.core.chemical.ResidueType method) lower_dihedrals() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) lower_edge_list_begin() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) lower_edge_list_end() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) lower_local() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) lower_neighbor_id() (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) lower_no_under() (pyrosetta.rosetta.utility.options.OptionCollection method) lower_numbered_node_symmetry_copy_index() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond method) lower_padding() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) lower_residue() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) lower_segment() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) lower_upper_connected_across_cutpoint() (in module pyrosetta.rosetta.core.scoring.methods) lower_value() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) lowercase() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) lowercased() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) lowest_score() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) lowest_score_pose() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) lowest_scores() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) lowres_reference_energy() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) lowval() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) lpad() (in module pyrosetta.rosetta.ObjexxFCL) lpadded() (in module pyrosetta.rosetta.ObjexxFCL) lstart() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) lstop() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) lstrip() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) lstrip_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) lstripped() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) lstripped_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) lt_dih() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) LT_Expression (class in pyrosetta.rosetta.numeric.expression_parser) LTE_Expression (class in pyrosetta.rosetta.numeric.expression_parser) LW_BaseDoubletOrientation (class in pyrosetta.rosetta.core.chemical.rna) lz() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method)

M

m1_b1_Ktheta() (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) m1_b1_theta0() (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) m1_b2_Ktheta() (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) m1_b2_theta0() (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) m1_m2_Ktheta() (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) m1_m2_theta0() (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) m2_b1_Ktheta() (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) m2_b1_theta0() (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) m2_b2_Ktheta() (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) m2_b2_theta0() (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) magentic_anisotropy_q_coeff() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) magentic_anisotropy_r_coeff() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) magnetic_anisotropy_effect() (in module pyrosetta.rosetta.core.scoring.rna.chemical_shift) main_atom() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) main_chain_torsion_set() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) main_chain_torsion_set_lists() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) main_chain_torsion_set_lists_real() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) main_chain_torsion_set_save() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) main_plain_mover() (in module pyrosetta.rosetta.protocols.jobdist) main_plain_pdb_mover() (in module pyrosetta.rosetta.protocols.jobdist) mainchain_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) mainchain_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) mainchain_dihedral_values() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) mainchain_potentials_match() (pyrosetta.rosetta.core.chemical.ResidueType method) mainchain_torsion() (pyrosetta.rosetta.core.conformation.Residue method) mainchain_torsions() (pyrosetta.rosetta.core.conformation.Residue method) MainChainTorsionSet (class in pyrosetta.rosetta.protocols.stepwise.modeler.protein) MainchainTorsionType (class in pyrosetta.rosetta.core.id) maintain_links() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) make() (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity method) make_asymmetric_movemap() (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) make_asymmetric_pose() (in module pyrosetta.rosetta.core.pose.symmetry) make_atom_map() (in module pyrosetta.rosetta.core.pose) make_atr_rep_grid() (in module pyrosetta.rosetta.protocols.ligand_docking) make_atr_rep_grid_without_ligand() (in module pyrosetta.rosetta.protocols.ligand_docking) make_atr_rep_grid_without_ligands() (in module pyrosetta.rosetta.protocols.ligand_docking) make_base_pair_aware_fold_tree() (in module pyrosetta.rosetta.protocols.dna) make_base_pair_mutation() (in module pyrosetta.rosetta.protocols.motifs) make_centroid() (in module pyrosetta.rosetta.core.chemical) make_chi_move() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) make_coarse_pose() (in module pyrosetta.rosetta.core.import_pose) make_compound_statement() (in module pyrosetta.rosetta.basic.database) make_conditional_index() (in module pyrosetta.rosetta.core.pack.dunbrack) make_continuous_true_regions_in_bool_vector() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) make_cut_at_moving_suite() (in module pyrosetta.rosetta.protocols.stepwise.modeler) make_Cx() (in module pyrosetta.rosetta.protocols.sic_dock) make_dna_mutations() (in module pyrosetta.rosetta.protocols.motifs) make_dna_rigid() (in module pyrosetta.rosetta.protocols.relax) make_extended_coarse_pose() (in module pyrosetta.rosetta.core.import_pose) make_hbBasetoAcc_unitvector() (in module pyrosetta.rosetta.core.scoring.hbonds) make_hotspot_foldtree() (in module pyrosetta.rosetta.protocols.protein_interface_design) make_index() (in module pyrosetta.rosetta.core.pack.dunbrack) make_initial_power_diagram() (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) make_interface_combos() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) make_jump() (pyrosetta.rosetta.core.kinematics.Jump method) make_local_bb_change() (pyrosetta.rosetta.protocols.loophash.LocalInserter method) (pyrosetta.rosetta.protocols.loophash.LocalInserter_SimpleMin method) make_local_bb_change_close_gaps() (pyrosetta.rosetta.protocols.loophash.LocalInserter method) (pyrosetta.rosetta.protocols.loophash.LocalInserter_SimpleMin method) make_local_bb_change_include_cut() (pyrosetta.rosetta.protocols.loophash.LocalInserter method) (pyrosetta.rosetta.protocols.loophash.LocalInserter_SimpleMin method) make_move() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) make_mutation() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) make_new_grid() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) make_new_sphere() (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) make_new_symmetric_PackerTask_by_requested_method() (in module pyrosetta.rosetta.core.pack) make_phosphate_nomenclature_matches_mini() (in module pyrosetta.rosetta.core.pose.rna) make_points() (in module pyrosetta.rosetta.numeric.kdtree) make_pose_from_frags() (in module pyrosetta.rosetta.core.fragment) make_pose_from_saccharide_sequence() (in module pyrosetta.rosetta.core.pose) make_pose_from_sequence() (in module pyrosetta.rosetta.core.pose) make_residue_mask_symmetric() (in module pyrosetta.rosetta.core.pose.symmetry) make_score_function_consistent_with_symmetric_state_of_pose() (in module pyrosetta.rosetta.core.pose.symmetry) make_segtag_with_dashes() (in module pyrosetta.rosetta.utility) make_semisymmetric_movemap() (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) make_sequence_shift() (pyrosetta.rosetta.protocols.loops.Loops method) make_simple_fold_tree_from_jump_frame() (in module pyrosetta.rosetta.core.fragment) make_specific_mutant() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) make_star_foldtree() (in module pyrosetta.rosetta.protocols.forge.methods) make_strand_info_str() (in module pyrosetta.rosetta.protocols.denovo_design.components) make_strand_neighbor_two() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) make_stub_scorefxn() (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) make_subdirs() (in module pyrosetta.rosetta.protocols.dna) make_sure_full_model_info_is_setup() (in module pyrosetta.rosetta.core.pose.full_model_info) make_sure_vdw_cached_rep_screen_info_is_setup() (in module pyrosetta.rosetta.protocols.scoring) make_symmetric_fibril() (in module pyrosetta.rosetta.protocols.fibril) make_symmetric_movemap() (in module pyrosetta.rosetta.core.pose.symmetry) make_symmetric_PackerTask_by_truncation() (in module pyrosetta.rosetta.core.pack) make_symmetric_pdb_info() (in module pyrosetta.rosetta.core.pose.symmetry) make_symmetric_pose() (in module pyrosetta.rosetta.core.pose.symmetry) make_symmetric_task() (in module pyrosetta.rosetta.core.pack) make_tag() (in module pyrosetta.rosetta.utility) make_tag_with_dashes() (in module pyrosetta.rosetta.utility) make_variants_match() (in module pyrosetta.rosetta.protocols.stepwise.modeler) make_vector() (in module pyrosetta.rosetta.utility.tools) make_vector1() (in module pyrosetta.rosetta.utility.tools) MakeABEGO_SS_Score (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeAmbigCSScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeAsymmetricStructureDataMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) MakeAtomPairConstraintsScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeBFactor (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeCanonicalHelix (class in pyrosetta.rosetta.protocols.membrane.benchmark) MakeConstScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeCSScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeDihedralConstraintsScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeDisulfideDistance (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeDisulfideIdentity (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeFragmentAllAtomCrmsd (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeFragmentChunkCrms (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeFragmentCrmsd (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeFragmentCrmsdResDepth (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeFragmentDME (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeFragmentScoringMethod (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeGunnCostScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeHydrophobicityProfileSimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeHydrophobicitySimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeInterbondAngleScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeJCoupling (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeLAMBEGO_Similarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeMidPhiOut (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeMidPsiOut (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakePartialSecondarySimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakePCS_FragDistance (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakePhi (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakePhiPsiRmsd (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakePhiPsiSquareWell (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeProlinePhiScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakePsi (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeRamaScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeRDCScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeRotLibJobInputter (class in pyrosetta.rosetta.protocols.make_rot_lib) MakeRotLibOptionsData (class in pyrosetta.rosetta.protocols.make_rot_lib) MakeRotLibPolymerType (class in pyrosetta.rosetta.protocols.make_rot_lib) MakeSecondaryIdentity (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeSecondarySimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeSequenceIdentity (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeSolventAccessibility (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeTalosSSSimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeTorsionBinSimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) manager() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) manipulate_cut_bias() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) manual_call() (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) map() (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringIntegerMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) map_by_residue_subsets() (in module pyrosetta.rosetta.protocols.fold_from_loops.utils) map_char_to_torsion_bin() (in module pyrosetta.rosetta.core.conformation) map_constraints_from_original_pose() (in module pyrosetta.rosetta.core.scoring.constraints) map_from_spectrum() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) map_of_weighted_scores() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) map_residues() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) map_seq1_seq2() (in module pyrosetta.rosetta.core.sequence) map_string_to_torsion_bin_string() (in module pyrosetta.rosetta.core.conformation) map_torsion_bin_to_char() (in module pyrosetta.rosetta.core.conformation) mapfile_activated() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) mapping() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) mapping_to_alignment() (in module pyrosetta.rosetta.core.sequence) mark() (pyrosetta.rosetta.protocols.pockets.ComparisonGrid method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) mark_as_cancelled() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) mark_as_default() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) mark_as_finished() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) mark_as_invalid() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) mark_as_test_run() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) mark_connect_incomplete() (pyrosetta.rosetta.core.conformation.Residue method) mark_current_job_id_for_repetition() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) mark_designable() (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) mark_energies_computed() (pyrosetta.rosetta.core.scoring.EnergyEdge method) mark_energies_uncomputed() (pyrosetta.rosetta.core.scoring.EnergyEdge method) mark_energy_computed() (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) mark_energy_uncomputed() (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) mark_incomplete() (pyrosetta.rosetta.core.chemical.ResConnID method) mark_job_as_having_begun() (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) mark_job_as_having_started() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter method) mark_leave_as_is() (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) mark_residue_moved() (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) mark_tags() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) markDepth() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) markEdgeDepth() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) markOneEdgeDepth() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) markPocketDepth() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) mask_asu() (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) mass() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.core.chemical.ResidueType method) match() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) match2D() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) match_dspos1 (class in pyrosetta.rosetta.protocols.match) match_possible_for_hit_geometry() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) match_variants() (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) MatchConstraintFileInfoList (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) MatchCounter (class in pyrosetta.rosetta.protocols.match) matched_tags() (pyrosetta.rosetta.core.io.silent.SilentFileData method) Matcher (class in pyrosetta.rosetta.protocols.match) MatchPositionModifier (class in pyrosetta.rosetta.protocols.match) MatchScoreWriter (class in pyrosetta.rosetta.protocols.match.output) MatrixMult() (in module pyrosetta.rosetta.numeric.model_quality) max() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.ObjexxFCL) (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.core.id.DOF_ID_Range method) (pyrosetta.rosetta.core.id.TorsionID_Range method) (pyrosetta.rosetta.numeric.random.RandomGenerator method) max_accepted_hbond_count() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) max_accepted_trials() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) max_allowed_oversaturated() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) max_angle_disp() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) max_angle_disp_4() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) max_angle_disp_7() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) max_angle_disp_slope() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) max_atom_radius() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) max_atomic_interaction_cutoff() (pyrosetta.rosetta.core.scoring.ScoreFunction method) max_atomic_interaction_distance() (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) max_atoms() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) max_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) max_bond_length() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) max_context_neighbor_cutoff() (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) max_cycles() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) max_dis() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) max_dis2() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) max_dist() (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) max_distance() (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) max_donated_hbond_count() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) max_frag_len() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) max_frag_length() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) max_heavy_heavy_cutoff() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) max_heavy_hydrogen_cutoff() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) max_hydrogen_hydrogen_cutoff() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) max_hydrogen_lj_radius() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) max_inter_ss_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) max_intra_ss_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) max_iter() (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) max_length() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) max_linear_chainbreak() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) max_network_size() (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) max_noe_distance() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) max_non_hydrogen_lj_radius() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) max_nstruct() (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) max_nstruct_index() (in module pyrosetta.rosetta.protocols.jd2) max_occurs() (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) max_per_move_torsion_delta_per_residue() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) max_pos() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) max_rad() (in module pyrosetta.rosetta.core.scoring.packstat) max_rms() (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) max_rotbump_energy() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) max_sample_iterations() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) max_score_diffs() (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) max_separation_dist_to_target_atom() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) max_size() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) max_size_col() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) max_total_torsion_delta_per_residue() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) max_trials() (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) max_tries_multiplier_for_ccd() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) max_valence_electrons_sp() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) max_values() (pyrosetta.rosetta.numeric.kdtree.KDPointList method) maxcycles() (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) maxtrials() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) may_change_aa() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.RenameAtom method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.Set_AA method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) maybe_initialize_handler() (in module pyrosetta.logging_support) mc() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) MC() (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) mc() (pyrosetta.rosetta.protocols.moves.TrialMover method) mc_accepted() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) mc_accepted_string() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) mc_accpeted() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) MCA (class in pyrosetta.rosetta.protocols.moves) mcfi() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) mean() (in module pyrosetta.rosetta.numeric) mean_and_stdev() (in module pyrosetta.rosetta.protocols.mpi_refinement) mean_squared_error() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) MeanField (class in pyrosetta.rosetta.protocols.mean_field) measure_rotamer_recovery() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) Medal_main() (in module pyrosetta.rosetta.protocols.medal) MedalExchange_main() (in module pyrosetta.rosetta.protocols.medal) MedalMover (class in pyrosetta.rosetta.protocols.medal) median() (in module pyrosetta.rosetta.numeric) meets_requirements() (pyrosetta.rosetta.core.chemical.Metapatch method) MEM (class in pyrosetta.rosetta.core.conformation.membrane) mem_all_atom_rmsd_no_super() (in module pyrosetta.rosetta.protocols.membrane) mem_all_atom_rmsd_with_super() (in module pyrosetta.rosetta.protocols.membrane) mem_bb_rmsd_no_super() (in module pyrosetta.rosetta.protocols.membrane) mem_bb_rmsd_with_super() (in module pyrosetta.rosetta.protocols.membrane) mem_cbeta_2TM_den12() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) mem_cbeta_2TM_den6() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) mem_cbeta_4TM_den12() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) mem_cbeta_4TM_den6() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) mem_cbeta_den12() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) mem_cbeta_den6() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) mem_env_log10() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) mem_env_log6() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) mem_foot_print() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) mem_footprint() (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) mem_pair_log() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) memb_dsolv1() (pyrosetta.rosetta.core.scoring.etable.MembEtable method) memb_dsolv2() (pyrosetta.rosetta.core.scoring.etable.MembEtable method) memb_lk_dgfree() (pyrosetta.rosetta.core.scoring.etable.MembEtable method) memb_lk_dgrefce() (pyrosetta.rosetta.core.scoring.etable.MembEtable method) memb_solv1() (pyrosetta.rosetta.core.scoring.etable.MembEtable method) memb_solv2() (pyrosetta.rosetta.core.scoring.etable.MembEtable method) Membed_init() (pyrosetta.rosetta.core.scoring.MembranePotential method) member_constraints() (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) MembEtable (class in pyrosetta.rosetta.core.scoring.etable) membrane() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) membrane_axis() (in module pyrosetta.rosetta.protocols.membrane) membrane_center() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) membrane_core() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) Membrane_FAEmbed (class in pyrosetta.rosetta.core.scoring) Membrane_FAEmbed_from_pose() (in module pyrosetta.rosetta.core.scoring) Membrane_FAPotential (class in pyrosetta.rosetta.core.scoring) membrane_info() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) membrane_jump() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) membrane_normal() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) membrane_normal_to_length_15() (in module pyrosetta.rosetta.protocols.membrane) membrane_rsd_num() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) membrane_steepness() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) membrane_thickness() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) MembraneAbinitio (class in pyrosetta.rosetta.protocols.abinitio) MembraneAbinitio.StageID (class in pyrosetta.rosetta.protocols.abinitio) MembraneCenterPerturbationMover (class in pyrosetta.rosetta.protocols.rigid) MembraneData (class in pyrosetta.rosetta.core.scoring.membrane) MembraneEmbed (class in pyrosetta.rosetta.core.scoring) MembraneEmbed_from_pose() (in module pyrosetta.rosetta.core.scoring) MembraneInfo (class in pyrosetta.rosetta.core.conformation.membrane) MembraneNormalPerturbationMover (class in pyrosetta.rosetta.protocols.rigid) MembranePositionFromTopologyMover (class in pyrosetta.rosetta.protocols.membrane) MembranePositionFromTopologyMoverCreator (class in pyrosetta.rosetta.protocols.membrane) MembranePotential (class in pyrosetta.rosetta.core.scoring) MembraneSpanConstraint (class in pyrosetta.rosetta.core.scoring.constraints) MembraneSpanConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) MembraneSpanTermZConstraint (class in pyrosetta.rosetta.core.scoring.constraints) MembraneTopology (class in pyrosetta.rosetta.protocols.simple_moves) MembraneTopology_from_pose() (in module pyrosetta.rosetta.core.scoring) memory_use() (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) Menv_penalties() (pyrosetta.rosetta.core.scoring.MembranePotential method) merge() (in module pyrosetta.rosetta.protocols.forge.methods) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.protocols.wum.WorkUnitList method) merge_behavior_manager() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) merge_constraints_from_cmdline() (in module pyrosetta.rosetta.core.scoring.constraints) merge_constraints_from_cmdline_to_pose() (in module pyrosetta.rosetta.core.scoring.constraints) merge_constraints_from_cmdline_to_scorefxn() (in module pyrosetta.rosetta.core.scoring.constraints) merge_fa_constraints_from_cmdline() (in module pyrosetta.rosetta.core.scoring.constraints) merge_fa_constraints_from_cmdline_to_pose() (in module pyrosetta.rosetta.core.scoring.constraints) merge_fa_constraints_from_cmdline_to_scorefxn() (in module pyrosetta.rosetta.core.scoring.constraints) merge_frags() (in module pyrosetta.rosetta.core.fragment) merge_in_other_pose() (in module pyrosetta.rosetta.protocols.stepwise.modeler) merge_in_other_pose_by_bond() (in module pyrosetta.rosetta.protocols.stepwise.modeler) merge_in_other_pose_by_jump() (in module pyrosetta.rosetta.protocols.stepwise.modeler) merge_residue_behavior (class in pyrosetta.rosetta.core.chemical) merge_two_poses() (in module pyrosetta.rosetta.protocols.stepwise.modeler) merge_two_poses_using_full_model_info() (in module pyrosetta.rosetta.protocols.stepwise.modeler) merge_vectors() (in module pyrosetta.rosetta.protocols.stepwise.modeler) mergeable() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) merged() (pyrosetta.rosetta.utility.options.OptionCollection method) metal_bond_angle_constraint_multiplier() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) metal_bond_dist_constraint_multiplier() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) metal_bond_LJ_multiplier() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) MetalContactsConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) MetaMaxExpression (class in pyrosetta.rosetta.numeric.expression_parser) MetaMinExpression (class in pyrosetta.rosetta.numeric.expression_parser) Metapatch (class in pyrosetta.rosetta.core.chemical) metapatch() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) metapatch_map() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) metapatches() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) method_type() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) method_weights() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) metric() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.TotalEnergyMetric method) MetricRecorder (class in pyrosetta.rosetta.protocols.canonical_sampling) MetricRecorderCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) metropolis_hastings_mover() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) MetropolisHastingsMover (class in pyrosetta.rosetta.protocols.canonical_sampling) MetropolisHastingsMoverCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) mg_calculation_annotated_sequence() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) mid_pos() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) middle_res() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) MidPhiOut (class in pyrosetta.rosetta.protocols.frag_picker.scores) midpoint() (pyrosetta.rosetta.protocols.loops.Loop method) MidPsiOut (class in pyrosetta.rosetta.protocols.frag_picker.scores) min() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.ObjexxFCL) (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.core.id.DOF_ID_Range method) (pyrosetta.rosetta.core.id.TorsionID_Range method) (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) min_atoms() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) min_bb() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) min_bb_set() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) min_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) min_bond_length() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) min_c_terminal_charges() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) min_client_rank() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) min_dis() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) min_dis2() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) min_dist() (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) min_distance() (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) min_heap() (pyrosetta.rosetta.protocols.cluster.Exemplar method) min_helix_length() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) min_inter_ss_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) min_intra_ss_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) min_length() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) min_mod() (in module pyrosetta.rosetta.protocols.cryst) min_n_terminal_charges() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) min_neighbor_sc() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) min_occurs() (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method)

min_options() (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) min_pack() (in module pyrosetta.rosetta.core.pack) min_pack_optimize() (in module pyrosetta.rosetta.core.pack) min_pack_place_opt_rotamers_on_pose() (in module pyrosetta.rosetta.core.pack) min_pack_setup() (in module pyrosetta.rosetta.core.pack) min_pair_data (class in pyrosetta.rosetta.core.scoring) min_pos() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) min_rb() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) min_rb_set() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) min_rms() (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) min_rotamers() (in module pyrosetta.rosetta.protocols.make_rot_lib) min_sc() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) min_sc_set() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) min_single_data (class in pyrosetta.rosetta.core.scoring) min_symm_dist2() (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) min_tolerance() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) min_type() (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) mini_pose_list() (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepLibrary method) minimization_graph() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) MinimizationEdge (class in pyrosetta.rosetta.core.scoring) MinimizationGraph (class in pyrosetta.rosetta.core.scoring) MinimizationNode (class in pyrosetta.rosetta.core.scoring) MinimizationRefiner (class in pyrosetta.rosetta.protocols.loop_modeling.refiners) minimize_after_delete() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) minimize_all() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) minimize_and_score_native_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) minimize_and_score_sugar() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) minimize_bond_angles() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) minimize_bond_lengths() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) minimize_cdrs() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) minimize_in_whole_structure_context() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) minimize_interface() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) minimize_magnesium_and_hydration_shell() (in module pyrosetta.rosetta.protocols.magnesium) minimize_no_bb() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) minimize_waters() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) minimize_with_constraints() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) MinimizeInterface() (in module pyrosetta.rosetta.protocols.protein_interface_design) Minimizer (class in pyrosetta.rosetta.core.optimization) minimizer_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) minimizer_rename_tag() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) MinimizerMode (class in pyrosetta.rosetta.protocols.stepwise.modeler) MinimizeStoredRBConfs (class in pyrosetta.rosetta.protocols.enzdes) MiniPose (class in pyrosetta.rosetta.core.pose) MinMover (class in pyrosetta.rosetta.protocols.minimization_packing) MinPackMover (class in pyrosetta.rosetta.protocols.minimization_packing) mintype() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) MinTypeEnum (class in pyrosetta.rosetta.protocols.antibody.design) minus_minus() (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator method) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.EdgeListIterator method) mirror_symm() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) mirror_symmetry() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) mirrored_relative_to_type() (pyrosetta.rosetta.core.conformation.Residue method) MirrorSymmetricConformation (class in pyrosetta.rosetta.core.conformation.symmetry) missing_atoms() (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder method) missing_dens_as_jump() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) missing_in_pose() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) MixtureFunc (class in pyrosetta.rosetta.core.scoring.func) MKDIR() (in module pyrosetta.rosetta.protocols.sparta) mm_atom_name() (pyrosetta.rosetta.core.conformation.Residue method) mm_atom_set() (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) mm_atom_type() (pyrosetta.rosetta.core.chemical.ResidueType method) mm_atom_type_index() (pyrosetta.rosetta.core.chemical.Atom method) mm_atom_type_name() (pyrosetta.rosetta.core.chemical.Adduct method) mm_atom_type_set() (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) mm_atom_types_ptr() (pyrosetta.rosetta.core.chemical.ResidueType method) mm_bond_angle_residue_type_param_set() (in module pyrosetta.rosetta.core.scoring.mm) mm_from_residues() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) mm_lj_library() (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) mm_lj_score() (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) mm_name() (pyrosetta.rosetta.core.chemical.Atom method) mm_type() (pyrosetta.rosetta.core.conformation.Atom method) MMAtomType (class in pyrosetta.rosetta.core.chemical) MMAtomTypeSet (class in pyrosetta.rosetta.core.chemical) MMBondAngleScore (class in pyrosetta.rosetta.core.scoring.mm) mmCIFJobOutputter (class in pyrosetta.rosetta.protocols.jd2) mmf_cat_in_datamap() (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) mmf_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) MMLJEnergyTable (class in pyrosetta.rosetta.core.scoring.mm) MMLJLibrary (class in pyrosetta.rosetta.core.scoring.mm) MMLJScore (class in pyrosetta.rosetta.core.scoring.mm) MMTorsionLibrary (class in pyrosetta.rosetta.core.scoring.mm) MMTorsionScore (class in pyrosetta.rosetta.core.scoring.mm) MNBRAK() (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) mod() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.ObjexxFCL) mode() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) model() (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) model_count() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) model_h3() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) model_ids() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) model_resnum() (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) model_with_density() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) ModelCDRH3 (class in pyrosetta.rosetta.protocols.antibody) modeler_sugar_at_five_prime() (in module pyrosetta.rosetta.protocols.stepwise.sampler.rna) modeler_sugar_at_three_prime() (in module pyrosetta.rosetta.protocols.stepwise.sampler.rna) ModelFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ModelNode (class in pyrosetta.rosetta.protocols.legacy_sewing) modeltag() (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.pose.PDBInfo method) modifiable() (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.moves.ResId method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) modifiable_residue_type_set_for_conf() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) modified2original_interval_endpoints() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) modified_match_positions() (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM method) (pyrosetta.rosetta.protocols.match.BfactorMPM method) (pyrosetta.rosetta.protocols.match.MatchPositionModifier method) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM method) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM method) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM method) (pyrosetta.rosetta.protocols.match.TaskOperationMPM method) ModifiedResidueInformation (class in pyrosetta.rosetta.core.io) modify() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) modify_after_jump() (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) modify_atom_properties_from_command_line() (in module pyrosetta.rosetta.core.chemical) modify_before_jump() (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) modify_ft_for_residue_insertion() (in module pyrosetta.rosetta.protocols.denovo_design.components) modify_impl() (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) modify_relative_filters_pdb_names() (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) modify_task() (pyrosetta.rosetta.core.pack.task.TaskFactory method) modify_unselected_residues() (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) modify_was_successful() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) ModifyStoredRBConfs (class in pyrosetta.rosetta.protocols.enzdes) ModifyVariantTypeMover (class in pyrosetta.rosetta.protocols.simple_moves) modp() (in module pyrosetta.rosetta.numeric.kinematic_closure) modres_map() (pyrosetta.rosetta.core.io.StructFileRep method) modrf() (in module pyrosetta.rosetta.numeric.kinematic_closure) modulo() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.utility) MolecularSurfaceCalculator (class in pyrosetta.rosetta.core.scoring.sc) moltenres() (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) moltenres_atomtree_collection() (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection method) momento_for_moltenres() (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) monopole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) monte_carlo() (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) monte_carlo_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.MonteCarloLoader method) MonteCarlo (class in pyrosetta.rosetta.protocols.moves) MonteCarloInterface (class in pyrosetta.rosetta.protocols.monte_carlo) MonteCarloLoader (class in pyrosetta.rosetta.protocols.parser) MonteCarloUtil (class in pyrosetta.rosetta.protocols.moves) more_precise_base_pair_classification() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) morpheme_from_ring_size() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) most_probable_bin() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) motif2scaffold_data (class in pyrosetta.rosetta.protocols.motif_grafting.movers) motif2scaffold_indexes (class in pyrosetta.rosetta.protocols.motif_grafting.movers) MotifMatchOverlapReq (class in pyrosetta.rosetta.core.scoring.motif) motifs_begin() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) motifs_end() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) movable_group() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) movable_jumps() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) move_all_inserted() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) move_apart() (in module pyrosetta.rosetta.protocols.docking) move_apart_first() (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) move_element() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) move_jumps_between_chains() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) move_ligand_neighbor_to_desired_position() (in module pyrosetta.rosetta.protocols.ligand_docking) move_ligand_to_desired_centroid() (in module pyrosetta.rosetta.protocols.ligand_docking) move_map() (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) move_map_action (class in pyrosetta.rosetta.core.select.movemap) move_map_from_loop() (in module pyrosetta.rosetta.protocols.loops) move_map_from_loops() (in module pyrosetta.rosetta.protocols.loops) move_pose_to_standard_orie() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) move_together() (in module pyrosetta.rosetta.protocols.docking) move_type (class in pyrosetta.rosetta.protocols.legacy_sewing) move_type() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) move_type_from_string() (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) moveable_jump() (in module pyrosetta.rosetta.core.pose.rna) MoveBeforeFilter (class in pyrosetta.rosetta.protocols.filters) moved() (pyrosetta.rosetta.core.scoring.EnergyNode method) MoveMap (class in pyrosetta.rosetta.core.kinematics) movemap() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) movemap_as_OP() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) movemap_builder_ct_namer() (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader method) movemap_cen() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) movemap_cen_all() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) movemap_cen_omegafixed() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) movemap_fa() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) movemap_fa_all() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) movemap_fa_omegafixed() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) movemap_factory() (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) movemap_factory_category() (in module pyrosetta.rosetta.core.select.movemap) movemap_from_blueprint() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) movemap_from_pose() (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) movemap_torsion_id_begin() (pyrosetta.rosetta.core.kinematics.MoveMap method) movemap_torsion_id_end() (pyrosetta.rosetta.core.kinematics.MoveMap method) MoveMapBuilderLoader (class in pyrosetta.rosetta.protocols.ligand_docking) MoveMapFactoryLoader (class in pyrosetta.rosetta.protocols.parser) MoveMapFactoryToNamedMoveMapMover (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) MovePoseToMembraneCenterMover (class in pyrosetta.rosetta.protocols.rigid) mover() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) mover_name() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) mover_or_add_group_name() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) mover_tag() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) mover_weight() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) MoverCreator (class in pyrosetta.rosetta.protocols.moves) movers() (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) MoverStatus (class in pyrosetta.rosetta.protocols.moves) moves_residue() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) MoveType (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) moving_res() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) mp_param() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) MPCbetaEnergy (class in pyrosetta.rosetta.core.scoring.membrane) MPCbetaEnergyCreator (class in pyrosetta.rosetta.core.scoring.membrane) MPDockingMover (class in pyrosetta.rosetta.protocols.docking.membrane) MPDockingMoverCreator (class in pyrosetta.rosetta.protocols.docking.membrane) MPDockingSetupMover (class in pyrosetta.rosetta.protocols.docking.membrane) MPDockingSetupMoverCreator (class in pyrosetta.rosetta.protocols.docking.membrane) MPEnvEnergy (class in pyrosetta.rosetta.core.scoring.membrane) MPEnvEnergyCreator (class in pyrosetta.rosetta.core.scoring.membrane) MPFastRelaxMoverCreator (class in pyrosetta.rosetta.protocols.relax.membrane) MPFindInterfaceMoverCreator (class in pyrosetta.rosetta.protocols.docking.membrane) MPHelicalityEnergy (class in pyrosetta.rosetta.core.scoring.membrane) MPHelicalityEnergyCreator (class in pyrosetta.rosetta.core.scoring.membrane) MPI_FILE_STATUS (class in pyrosetta.rosetta.utility.io.mpi_stream) mpi_finalize() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) mpi_npes() (in module pyrosetta.rosetta.protocols.wum) mpi_nprocs() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) mpi_rank() (in module pyrosetta.rosetta.protocols.wum) (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) MPI_ranks_handling_message() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) MPI_reroute_rank() (pyrosetta.rosetta.utility.io.ozstream method) mpi_safe_std_err() (in module pyrosetta.rosetta.utility.options) MPI_STREAM_MSG (class in pyrosetta.rosetta.utility.io.mpi_stream) mpi_tags (class in pyrosetta.rosetta.basic.mpi) MPIArchiveJobDistributor (class in pyrosetta.rosetta.protocols.jd2.archive) MPIFileBufJobDistributor (class in pyrosetta.rosetta.protocols.jd2) MPIMultiCommJobDistributor (class in pyrosetta.rosetta.protocols.jd2) MPIWorkPartitionJobDistributor (class in pyrosetta.rosetta.protocols.jd2) MPIWorkPoolJobDistributor (class in pyrosetta.rosetta.protocols.jd2) MPLipidAccessibility (class in pyrosetta.rosetta.protocols.membrane) MPLipoEnergy (class in pyrosetta.rosetta.core.scoring.membrane) MPLipoEnergyCreator (class in pyrosetta.rosetta.core.scoring.membrane) MPMutateRelaxMoverCreator (class in pyrosetta.rosetta.protocols.membrane) MPNonHelixPenalty (class in pyrosetta.rosetta.core.scoring.membrane) MPNonHelixPenaltyCreator (class in pyrosetta.rosetta.core.scoring.membrane) MPPairEnergy (class in pyrosetta.rosetta.core.scoring.membrane) MPPairEnergyCreator (class in pyrosetta.rosetta.core.scoring.membrane) MPQuickRelaxMoverCreator (class in pyrosetta.rosetta.protocols.membrane) MPResidueLipophilicityEnergy (class in pyrosetta.rosetta.core.scoring.membrane) MPResidueLipophilicityEnergyCreator (class in pyrosetta.rosetta.core.scoring.membrane) MPSymDockMoverCreator (class in pyrosetta.rosetta.protocols.symmetric_docking.membrane) MPTerminiPenalty (class in pyrosetta.rosetta.core.scoring.membrane) MPTerminiPenaltyCreator (class in pyrosetta.rosetta.core.scoring.membrane) MPTMProjPenalty (class in pyrosetta.rosetta.core.scoring.membrane) MPTMProjPenaltyCreator (class in pyrosetta.rosetta.core.scoring.membrane) msas_for_atom() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) msg() (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.utility.excn.BadInput method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) mstype_from_name() (in module pyrosetta.rosetta.protocols.moves) mu() (pyrosetta.rosetta.core.pose.Pose method) MulliganPNearEvaluator (class in pyrosetta.rosetta.protocols.toolbox) multi_cool_annealer() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) multi_cool_annealer_history_size() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) multi_fast_relax() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) multi_relative() (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) multi_use() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) MultiConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) MultiDimensionalHistogram (class in pyrosetta.rosetta.numeric) Multifunc (class in pyrosetta.rosetta.core.optimization) MultipleDomainMover (class in pyrosetta.rosetta.protocols.rna.denovo.coarse) MultipleSigmoids (class in pyrosetta.rosetta.protocols.calc_taskop_filters) MultipoleAxisType (class in pyrosetta.rosetta.core.scoring) MultipoleElecPoseInfo (class in pyrosetta.rosetta.core.scoring) MultipoleElecResidueInfo (class in pyrosetta.rosetta.core.scoring) MultipoleElecRotamerSetInfo (class in pyrosetta.rosetta.core.scoring) MultiStatePacker (class in pyrosetta.rosetta.protocols.multistate_design) MultiTemperatureTrialCounter (class in pyrosetta.rosetta.protocols.canonical_sampling) multivec2poseBfacts() (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) multstubs() (in module pyrosetta.rosetta.protocols.sic_dock) must_switch_bins() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) mutants_begin() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) mutants_end() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) mutate() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) mutate_all_at_once() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) mutate_loops_for_search() (in module pyrosetta.rosetta.protocols.motifs) mutate_position() (in module pyrosetta.rosetta.core.pose.rna) mutate_position_vector_for_search() (in module pyrosetta.rosetta.protocols.motifs) mutate_res_if_allowed() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) mutate_residue() (in module pyrosetta.toolbox) MutateFrameworkForCluster (class in pyrosetta.rosetta.protocols.antibody.design) MutateResidue (class in pyrosetta.rosetta.protocols.simple_moves) mutation_ddGs() (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) mutation_rate() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) MutationSetDesignOperation (class in pyrosetta.rosetta.protocols.task_operations) my_group() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) my_itr() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) my_local_coord_frame() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) my_residue_pair_energy() (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method)

N

N() (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) n() (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) n_active_score_types() (pyrosetta.rosetta.core.scoring.EnergyGraph method) n_ang_U1D2_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) n_ang_U2D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) n_atom() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) N_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) n_atomtypes() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) n_bonded_neighbor_all_res() (pyrosetta.rosetta.core.conformation.Residue method) n_ca() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) n_ca_bond() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) n_ca_c() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) n_ca_c_angle() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) n_children() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) n_clusters_from_last_run() (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringProtocol method) n_columns() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) n_correctly_aligned_positions() (in module pyrosetta.rosetta.core.sequence) n_current_residue_connections() (pyrosetta.rosetta.core.conformation.Residue method) n_cycles() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) n_default_value() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) n_dependencies() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) n_designed() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) n_dis_U1D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) n_elements() (pyrosetta.rosetta.core.chemical.ElementSet method) n_external_samplers() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) n_fragment_eval() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) n_fragment_gen() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) n_geometric_constraints() (pyrosetta.rosetta.protocols.match.Matcher method) n_hbond_acceptors() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) n_hbond_donors() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) n_hbonds() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) n_helices() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) n_input_sources() (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) n_key() (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) n_loops() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) n_lower() (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) n_mainchain_atoms() (pyrosetta.rosetta.core.conformation.Residue method) n_mutants() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) n_non_polymeric_residue_connections() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) n_nonchitip_atoms_for_chi() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) n_nonjump_children() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) n_nus() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) n_omega() (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) n_orbitals() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) n_parameters() (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) n_parameters_sets() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) n_part() (pyrosetta.rosetta.utility.options.OptionCollection method) n_part_prefix_match() (pyrosetta.rosetta.utility.options.OptionCollection method) n_polymeric_residue_connections() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) n_possible_hits_per_upstream_conformation() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) n_possible_residue_connections() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) n_property_sets() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) n_proton_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) n_protons() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) n_real_dofs() (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) n_reference_pose() (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) n_residue() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) n_residue_connections_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) n_residues() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) n_residues_after_cutpoint() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) n_residues_before_cutpoint() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) n_ring_conformer_sets() (pyrosetta.rosetta.core.chemical.ResidueType method) n_rings() (pyrosetta.rosetta.core.chemical.ResidueType method) n_rows() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) n_sample() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) n_samples_per_side_of_nrchi_bin() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) n_samples_wi_sd_range() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) n_scores() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) n_segment() (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) n_sequence_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) n_temp_levels() (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) n_terminal_constraint_strength() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) n_terminus_size() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) n_tor_U1D3_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) n_tor_U2D2_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) n_tor_U3D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) n_torsion_sets() (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) n_torsions() (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) n_torsions_total() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) n_trees() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) n_types() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) n_unassigned() (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) n_upper() (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) n_value() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) n_virtual_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) n_xyz() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) na_analogue() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) nali() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) name() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.ElementSet method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.MMAtomType method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.RenameAtom method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.Set_AA method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AROMATIC method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.CHARGED method) (pyrosetta.rosetta.core.pack.task.EMPTY method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NC method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.PIKRNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PROPERTY method) (pyrosetta.rosetta.core.pack.task.RESET method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.TotalEnergyMetric method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method)

name1() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) name2suite() (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) name3() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) name3_from_oneletter() (in module pyrosetta.rosetta.protocols.motifs) name_for_common_type() (in module pyrosetta.rosetta.utility.tag) name_from_aa() (in module pyrosetta.rosetta.core.chemical) name_from_database_mode() (in module pyrosetta.rosetta.utility.sql_database) name_from_elements() (in module pyrosetta.rosetta.core.chemical.element) name_from_foldtype() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) name_from_score_type() (in module pyrosetta.rosetta.core.scoring) name_from_transaction_mode() (in module pyrosetta.rosetta.utility.sql_database) name_map() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) name_mapOP() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) name_static() (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.TotalEnergyMetric method) name_to_listener_tag() (in module pyrosetta.rosetta.basic.mpi) name_wo_rgstr() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) named_atom_id_to_atom_id() (in module pyrosetta.rosetta.core.conformation) (in module pyrosetta.rosetta.core.pose) named_stub_id_to_stub_id() (in module pyrosetta.rosetta.core.pose) NamedAngleConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) NamedAtomID (class in pyrosetta.rosetta.core.id) NamedAtomPairConstraintCreator (class in pyrosetta.rosetta.protocols.constraints_additional) NamedSegmentSelector (class in pyrosetta.rosetta.protocols.denovo_design.residue_selectors) NamedStubID (class in pyrosetta.rosetta.core.id) nangles() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) NATAA (class in pyrosetta.rosetta.core.pack.task) NatbiasSecondaryStructureEnergy (class in pyrosetta.rosetta.protocols.fldsgn.potentials.sspot) NatbiasStrandPairPotential (class in pyrosetta.rosetta.protocols.fldsgn.potentials.sspot) native_CA_gdtmm() (in module pyrosetta.rosetta.core.scoring) native_CA_rmsd() (in module pyrosetta.rosetta.core.scoring) native_distance_viol() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) native_edensity_score_cutoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) native_loop_core_CA_rmsd() (in module pyrosetta.rosetta.protocols.loops) native_positions() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) native_secstruct() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) native_tag() (pyrosetta.rosetta.protocols.jobdist.BasicJob method) NativeAntibodySeq (class in pyrosetta.rosetta.protocols.antibody.design) NativeEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) natives_select() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) natom() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) natom_aligned() (in module pyrosetta.rosetta.protocols.hybridization) natoms() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) NATRO (class in pyrosetta.rosetta.core.pack.task) nb_list() (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) nbb() (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) nblist() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) nblist_dis2_cutoff_HH() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) nblist_dis2_cutoff_XH() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) nblist_dis2_cutoff_XX() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) nbonds() (pyrosetta.rosetta.core.chemical.ResidueType method) nbonds_from_bb_atom() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) nbr_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) nbr_atom_rmsd() (in module pyrosetta.rosetta.core.scoring) nbr_atom_xyz() (pyrosetta.rosetta.core.conformation.Residue method) nbr_e_threshold() (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) nbr_radius() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) nbr_vertex() (pyrosetta.rosetta.core.chemical.ResidueType method) nbrs() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) NC (class in pyrosetta.rosetta.core.pack.task) NCAARotLibBBTorsions (class in pyrosetta.rosetta.core.chemical) NCAARotLibNumRotamerBins (class in pyrosetta.rosetta.core.chemical) NCAARotLibPath (class in pyrosetta.rosetta.core.chemical) NCaCaC_Dihedral_Func (class in pyrosetta.rosetta.core.scoring.disulfides) ncbb_design_main_loop() (in module pyrosetta.rosetta.protocols.ncbb) nchi() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) ncluster() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) nContinuousSegments() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) NCSResMapping (class in pyrosetta.rosetta.protocols.symmetry) ncsts() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) ncycle() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) ndihe() (pyrosetta.rosetta.core.chemical.ResidueType method) ndims() (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) nDoFs() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) ndots() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) nearby_atom_cut() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) nearby_atom_cutoff() (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) nearest_atom_for_constraint() (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) nearest_neighbor() (in module pyrosetta.rosetta.numeric.kdtree) nearest_neighbors() (in module pyrosetta.rosetta.numeric.kdtree) nearest_ssize() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.ObjexxFCL) neg_space_element_allocation_error_message() (in module pyrosetta.rosetta.utility.graph) negate() (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) neighbor_count() (in module pyrosetta.rosetta.protocols.sic_dock) neighbor_cutoff() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) neighbor_detection_dis() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) neighbor_dis() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) neighbor_hits() (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) neighbor_id() (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) neighbor_iterator_begin() (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) neighbor_iterator_end() (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) neighbor_min() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) neighbor_min_add() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) neighbor_min_clear() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) neighbor_strands() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) NeighborDependentTabooSamplingKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) NeighborDependentTorsionSamplingKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) Neighborhood (class in pyrosetta.rosetta.protocols.neighbor) neighborhood_calc() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) NeighborhoodByDistanceCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) NeighborhoodResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) neighboring_atoms() (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) NeighborList (class in pyrosetta.rosetta.core.scoring) neighbors() (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) NeighborsByDistanceCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) Nend_orient() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) Nend_pos() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) net_formal_charge() (pyrosetta.rosetta.core.chemical.ResidueType method) netcharge_setup_file() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) netcharge_setup_file_count() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) NetChargeEnergy (class in pyrosetta.rosetta.core.scoring.netcharge_energy) NetChargeEnergySetup (class in pyrosetta.rosetta.core.scoring.netcharge_energy) netTargetPocketVolume() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) network_analysis() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) network_analysis2() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) network_anchoring() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) network_anchoring_per_residue() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) network_contains_aa() (in module pyrosetta.rosetta.protocols.hbnet) new_chain_order() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) new_chemical_bond() (pyrosetta.rosetta.core.kinematics.FoldTree method) new_decoy() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) new_entity() (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator method) new_fold_tree_initializer() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) new_icoor() (pyrosetta.rosetta.core.chemical.Orbital method) new_jump() (pyrosetta.rosetta.core.kinematics.FoldTree method) new_omega() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) new_orbital_icoor_data() (pyrosetta.rosetta.core.chemical.ResidueType method) new_phi() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) new_positions() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) new_psi() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) new_secondary_structure_override() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) new_sequence_override() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) new_sfr() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) new_sym_min() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) newDataLoader() (pyrosetta.rosetta.protocols.parser.DataLoaderFactory method) newTopologyClaimer() (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory method) next() (pyrosetta.rosetta.core.chemical.AutomorphismIterator method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) next_angle() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) next_child() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) next_job() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) next_resnum() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) next_segment_id() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) next_torsion_string() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) nfft() (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) ngroups() (pyrosetta.rosetta.protocols.symmetry.NCSResMapping method) nhbonds() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) nheavyatoms() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) nint() (in module pyrosetta.rosetta.ObjexxFCL) niter() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) nl_if() (in module pyrosetta.rosetta.ObjexxFCL.format) nlevels_per_dim() (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) nloop() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) nmodes() (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) nmoltenres() (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) nmoves() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) nmtr() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) NO_ADDUCTS (class in pyrosetta.rosetta.core.pack.task) no_chainend_ter() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) no_design() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) no_detect_pseudobonds() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) no_optH() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) no_output_cen() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) no_relax() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) NoClient (class in pyrosetta.rosetta.utility.keys) NoDefault() (pyrosetta.rosetta.utility.options.BooleanOption method) nodeindex_to_residue_memory_address() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) nodes() (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) NoesyModule (class in pyrosetta.rosetta.protocols.noesy_assign) NoFailDataMap (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts) NomenclatureManager (class in pyrosetta.rosetta.core.io) non_const_pose() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) non_helix_in_membrane_penalty() (pyrosetta.rosetta.core.scoring.MembranePotential method) non_ideal() (pyrosetta.rosetta.protocols.loophash.FastGapMover method) non_main_chain_sugar_coords() (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) non_main_chain_sugar_coords_defined() (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) non_peptide_heavy_atom_RMSD() (in module pyrosetta.rosetta.core.scoring) non_virtual_score() (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) nonadduct_variants_match() (in module pyrosetta.rosetta.core.chemical) noncanonical_atom_count() (in module pyrosetta.rosetta.core.pose) noncanonical_chi_count() (in module pyrosetta.rosetta.core.pose) noncanonical_residue_count() (in module pyrosetta.rosetta.core.pose) nonchitip_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) nonchitip_atoms() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) nonconst_atom() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) nonconst_atom_numbers_for_mg_calculation() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) nonconst_atom_numbers_for_vdw_calculation() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) nonconst_atoms() (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) nonconst_begin() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) nonconst_cenlist_from_pose() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) nonconst_circle() (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) nonconst_data() (pyrosetta.rosetta.core.conformation.Residue method) nonconst_data_ptr() (pyrosetta.rosetta.core.conformation.Residue method) nonconst_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_direction() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) nonconst_downstream_algorithms() (pyrosetta.rosetta.protocols.match.Matcher method) nonconst_end() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) nonconst_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) nonconst_generators() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) nonconst_id() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) nonconst_induced_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_induced_rf_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_inner_job() (pyrosetta.rosetta.protocols.jd3.LarvalJob method) nonconst_interface_from_pose() (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) nonconst_is_buried() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) nonconst_is_interface() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) nonconst_is_magnesium() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) nonconst_long_range_container() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) nonconst_Membrane_FAEmbed_from_pose() (in module pyrosetta.rosetta.core.scoring) nonconst_MembraneEmbed_from_pose() (in module pyrosetta.rosetta.core.scoring) nonconst_MembraneTopology_from_pose() (in module pyrosetta.rosetta.core.scoring) nonconst_monopole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_mp_param() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_other_struct_list() (pyrosetta.rosetta.core.io.silent.SilentStruct method) nonconst_partners() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) nonconst_power() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) nonconst_quadrupole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_rad() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) nonconst_rad2() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) nonconst_res() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) nonconst_resA() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) nonconst_resB() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) nonconst_residue_task() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) nonconst_rKirkwood() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_rna_scoring_info_from_pose() (in module pyrosetta.rosetta.core.scoring.rna) nonconst_rna_task() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) nonconst_rosetta_res_type() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_rotamer() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) nonconst_stored_induced_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_stored_induced_rf_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_vdw_cached_rep_screen_info_from_pose() (in module pyrosetta.rosetta.protocols.scoring) nonconst_vdw_type() (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) nonconst_xyz() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) NonContinuousFrame (class in pyrosetta.rosetta.core.fragment) nondefault() (pyrosetta.rosetta.core.chemical.ResidueType method) nonlocal_pairs() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) NonlocalFrags_main() (in module pyrosetta.rosetta.protocols.frag_picker.nonlocal) NonlocalPair (class in pyrosetta.rosetta.protocols.frag_picker.nonlocal) nonmatching_residues() (in module pyrosetta.rosetta.core.io.external) nonmonotone() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) nonnegative_principal_angle_degrees() (in module pyrosetta.rosetta.numeric) nonpivot_residues() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) NonResidueTypeConstraint (class in pyrosetta.rosetta.core.scoring.constraints) nonzero_deltas() (pyrosetta.rosetta.core.kinematics.Jump method) nonzero_hbond_weight() (in module pyrosetta.rosetta.core.scoring.hbonds) nooutput() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) NoOutputJobOutputter (class in pyrosetta.rosetta.protocols.jd2) NoRepackDisulfides (class in pyrosetta.rosetta.core.pack.task.operation) norm() (in module pyrosetta.rosetta.numeric.kinematic_closure) norm_factor() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) norm_squared() (pyrosetta.rosetta.core.scoring.EMapVector method) normal() (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) normal_to_ellipsoid() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) normalize_to_thk() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) normalized_distance_in_degrees() (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) normalized_peak_volume() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) NormalizedEvaluatedArchive (class in pyrosetta.rosetta.protocols.jd2.archive) normalizing_area() (in module pyrosetta.rosetta.core.scoring) normalizing_area_total() (in module pyrosetta.rosetta.core.scoring) normalizing_area_total_hydrophobic_atoms_only() (in module pyrosetta.rosetta.core.scoring) normalizing_area_total_polar_atoms_only() (in module pyrosetta.rosetta.core.scoring) NormalModeMinimizer (class in pyrosetta.rosetta.protocols.normalmode) NormalModeMultifunc (class in pyrosetta.rosetta.protocols.normalmode) not_already_connected() (in module pyrosetta.rosetta.protocols.dna) not_blank() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) not_empty() (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) not_end() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) not_unbounded() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) not_universal_main() (in module pyrosetta.rosetta.protocols.jobdist) not_using() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) not_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) NOTAA (class in pyrosetta.rosetta.core.pack.task) note_coordinate_change_registered() (pyrosetta.rosetta.core.kinematics.AtomTree method) note_hit_geometry() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) note_job_completed() (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) note_long_range_interactions_exist_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) note_rpe_calculated() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) note_short_range_interactions_exist_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) note_submatrix_accessed() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) note_submatrix_added() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) note_vertex_reached() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) notify() (in module pyrosetta.rosetta.ObjexxFCL.internal.ObserverMediator) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) notify_destructed() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) notify_energy_change() (pyrosetta.rosetta.protocols.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborsByDistanceCalculator method) notify_structure_change() (pyrosetta.rosetta.protocols.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborsByDistanceCalculator method) NotJumpSelector (class in pyrosetta.rosetta.core.select.jump_selector) NotResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) npd_hb_eval_type_weight() (in module pyrosetta.rosetta.core.scoring.hbonds) npd_hb_weight() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) npd_hbond_set() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) NPDHBondEnergy (class in pyrosetta.rosetta.core.scoring.hbonds) NPDHBondSet (class in pyrosetta.rosetta.core.scoring.hbonds) NPDHBSimpleInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) NPDPropCalculator (class in pyrosetta.rosetta.protocols.pack_daemon) nr_frags() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) nr_frames() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) nr_moves() (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) nr_open_slaves() (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) nr_res_affected() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) nr_residues() (pyrosetta.rosetta.protocols.loops.Loops method) NRbisafe() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) nrchi_prob_minimum_for_extra_samples() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) nread_limit_for_file() (pyrosetta.rosetta.utility.io.FileContentsMap method) nreads_for_file() (pyrosetta.rosetta.utility.io.FileContentsMap method) nres() (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) nres_protein() (in module pyrosetta.rosetta.core.pose) nrot() (pyrosetta.rosetta.protocols.mean_field.AAProb method) nshells_for_atom() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) nsol() (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) nstrand_values() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) nstruct() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) nstruct_centroid() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) nstruct_index() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) nstruct_max() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) nterm_included() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) ntrials() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) ntries() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) nu() (pyrosetta.rosetta.core.conformation.Residue method) nu1_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) nu1_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) nu2_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) nu2_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) nu_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) NubInitioLoopClosureMover (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) NubInitioMoverCreator (class in pyrosetta.rosetta.protocols.fold_from_loops) NucleotideMutation (class in pyrosetta.rosetta.protocols.evolution) NullPerturber (class in pyrosetta.rosetta.protocols.denovo_design.components) NullPoseFolder (class in pyrosetta.rosetta.protocols.denovo_design.components) NullResourceLocator (class in pyrosetta.rosetta.basic.resource_manager.locator) NullResourceLocatorCreator (class in pyrosetta.rosetta.basic.resource_manager.locator) NullStream (class in pyrosetta.rosetta.basic.resource_manager.locator) num_accepted_scores() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) num_accepts() (pyrosetta.rosetta.protocols.moves.TrialMover method) num_atoms() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) num_bins() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) num_bondangles() (pyrosetta.rosetta.core.chemical.ResidueType method) num_bulge() (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepSequence method) num_chains() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.frags.VallData method) num_chi_angles() (in module pyrosetta.rosetta.core.pose) num_chunk_sets() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) num_chunks() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) num_cutpoint() (pyrosetta.rosetta.core.kinematics.FoldTree method) num_designable() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) num_dimensions() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) num_domains() (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) num_donor_acceptor_groups() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) num_edges() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) num_elements() (pyrosetta.rosetta.utility.recent_history_queue method) num_fragpick() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) num_geom_cst() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) num_hbond_acceptors() (in module pyrosetta.rosetta.core.pose) num_hbond_donors() (in module pyrosetta.rosetta.core.pose) num_heavy_atoms() (in module pyrosetta.rosetta.core.pose) num_iterations() (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) num_jump() (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) num_lines_in_file() (in module pyrosetta.rosetta.protocols.cluster.calibur) num_loop() (pyrosetta.rosetta.protocols.loops.Loops method) num_loops() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) num_mcfis() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) num_moving_chunks() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) num_negative_states() (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) num_neighbors() (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) num_neighbors_counting_self() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) num_neighbors_counting_self_static() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) num_nodes() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) num_packed() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) num_pairings() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) num_pose_minimize() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) num_poses() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) num_positions() (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) num_positive_states() (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) num_pts() (pyrosetta.rosetta.protocols.cluster.APCluster method) num_random_samples() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) num_rejections() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) num_residues() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) num_rings() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) num_rotamers() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) num_segments() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) num_selectors() (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) num_seqpos_lists() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) num_states() (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) num_steps() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) num_strands() (in module pyrosetta.rosetta.protocols.denovo_design.components) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) num_strings() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) num_target_states() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) num_to_be_packed() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) num_trials() (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) num_triggers() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) num_try_div() (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) number() (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer method) number_bonded_heavyatoms() (pyrosetta.rosetta.core.chemical.ResidueType method) number_bonded_hydrogens() (pyrosetta.rosetta.core.chemical.ResidueType method) number_heavy_chain() (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) number_light_chain() (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) number_of_atoms() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) number_of_high_resolution_cycles() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) number_of_residues() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) Numberer (class in pyrosetta.rosetta.protocols.antibody.grafting) numbering_scheme() (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) numbering_scheme_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) numbering_scheme_is_present() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) numbering_scheme_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) numchanges() (in module pyrosetta.rosetta.numeric.kinematic_closure) numeric_properties() (pyrosetta.rosetta.core.chemical.ResidueProperties method) numerical_derivative_check() (in module pyrosetta.rosetta.core.optimization) (in module pyrosetta.rosetta.core.optimization.symmetry) numGaussians() (pyrosetta.rosetta.core.scoring.func.USOGFunc method) NumNeighborsMPM (class in pyrosetta.rosetta.protocols.match) numpy_to_rosetta() (in module pyrosetta.toolbox.numpy_utils) numroots() (in module pyrosetta.rosetta.numeric.kinematic_closure) nus() (pyrosetta.rosetta.core.conformation.Residue method) nusing() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) nvar() (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method)

O

O() (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) o2prime_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) o2prime_legacy_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) o2prime_trials() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) o3prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) o4prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) o5prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) O_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) obey_ENDMDL() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) observe_after_metropolis() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) Observer (class in pyrosetta.rosetta.ObjexxFCL) observer_attached() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) observer_cache() (pyrosetta.rosetta.core.pose.Pose method) observer_p() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) ObserverCache (class in pyrosetta.rosetta.core.pose.datacache) ObserverGraph (class in pyrosetta.rosetta.ObjexxFCL.internal) ObserverMulti (class in pyrosetta.rosetta.ObjexxFCL) ObserverSingle (class in pyrosetta.rosetta.ObjexxFCL) obsolete() (pyrosetta.rosetta.core.pose.PDBInfo method) obtain_rtypes_for_target_sequence() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) occ_space_hash() (pyrosetta.rosetta.protocols.match.Matcher method) OccFitParam (class in pyrosetta.rosetta.core.scoring.geometric_solvation) occupancy() (pyrosetta.rosetta.core.pose.PDBInfo method) OccupiedSpaceHash (class in pyrosetta.rosetta.protocols.match) ocstream (class in pyrosetta.rosetta.utility.io) off_rotamer_pack() (in module pyrosetta.rosetta.core.pack) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) off_rotamer_pack_optimize() (in module pyrosetta.rosetta.core.pack) off_rotamer_pack_setup() (in module pyrosetta.rosetta.core.pack) off_rotamer_pack_update_pose() (in module pyrosetta.rosetta.core.pack) offset() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) OffsetPeriodicBoundFunc (class in pyrosetta.rosetta.core.scoring.constraints) old_seqpos() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) omega() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) omega0() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) omega0_copies_pitch_instead() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) omega1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) OmegaPreferenceSamplingData (class in pyrosetta.rosetta.core.scoring.carbohydrates) OmegaPreferencesFunction (class in pyrosetta.rosetta.core.scoring.carbohydrates) OmegaPreferenceType (class in pyrosetta.rosetta.core.scoring.carbohydrates) on_connection_change() (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) on_identity_change() (pyrosetta.rosetta.core.pose.PDBInfo method) on_length_change() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) on_new_fragments() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) on_pose_conf_change() (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) on_pose_destruction_change() (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) on_pose_energy_change() (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) on_residue_append() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) on_residue_delete() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) on_residue_prepend() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) on_segment() (in module pyrosetta.rosetta.core.membrane) one_letter_sequence() (pyrosetta.rosetta.core.io.silent.SilentStruct method) one_line_report() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) one_random_loop() (pyrosetta.rosetta.protocols.loops.Loops method) onebody_energies() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) OneGaussianScattering (class in pyrosetta.rosetta.core.scoring.electron_density) (class in pyrosetta.rosetta.core.scoring.fiber_diffraction) oneletter_code_from_aa() (in module pyrosetta.rosetta.core.chemical) oneletter_code_specifies_aa() (in module pyrosetta.rosetta.core.chemical) onError() (in module pyrosetta.rosetta.core.pack.task) OneToAllEnergyContainer (class in pyrosetta.rosetta.core.scoring) OneToAllNeighborConstIterator (class in pyrosetta.rosetta.core.scoring) OneToAllNeighborIterator (class in pyrosetta.rosetta.core.scoring) only_clean_seq_num() (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) op() (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) op1_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) op2_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) open() (in module pyrosetta.rosetta.basic.database) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ozstream method) open_append() (pyrosetta.rosetta.utility.io.ozstream method) open_append_if_existed() (pyrosetta.rosetta.utility.io.ozstream method) operate_on_ex1() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) operate_on_ex2() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) operate_on_ex3() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) operate_on_ex4() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) OperateOnResidueSubset (class in pyrosetta.rosetta.core.pack.task.operation) Operation (class in pyrosetta.rosetta.protocols.calc_taskop_filters) operation() (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) Operator (class in pyrosetta.rosetta.protocols.calc_taskop_filters) operator_filter() (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) OptCysHG (class in pyrosetta.rosetta.core.pack.task.operation) OptEData (class in pyrosetta.rosetta.protocols.optimize_weights) OptEMultifunc (class in pyrosetta.rosetta.protocols.optimize_weights) OptEMultifuncMPIMessages (class in pyrosetta.rosetta.protocols.optimize_weights) OptEPositionData (class in pyrosetta.rosetta.protocols.optimize_weights) OptEPositionDataType (class in pyrosetta.rosetta.protocols.optimize_weights) OptH (class in pyrosetta.rosetta.core.pack.task.operation) optimal_connection_point() (in module pyrosetta.rosetta.protocols.protein_interface_design) optimize_branch_angles() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) optimize_foldtree() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) optimize_h() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) optimize_H_and_notify() (in module pyrosetta.rosetta.core.pack) optimizeH() (in module pyrosetta.rosetta.core.pack) OptimizeMembranePositionMoverCreator (class in pyrosetta.rosetta.protocols.membrane) OptimizeProteinEmbeddingMoverCreator (class in pyrosetta.rosetta.protocols.membrane) Option (class in pyrosetta.rosetta.utility.options) option() (pyrosetta.rosetta.utility.options.OptionCollection method) option_vdw_rep_screen_info_user() (in module pyrosetta.rosetta.protocols.scoring) optional_name_attribute() (in module pyrosetta.rosetta.utility.tag) optional_output_name() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) optional_positive_intafteroption() (in module pyrosetta.rosetta.basic.options) OptionCollection (class in pyrosetta.rosetta.utility.options) OptionKey (class in pyrosetta.rosetta.utility.options) options() (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) OptionTypes (class in pyrosetta.rosetta.utility.options) or_adducts() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) OR_combine() (in module pyrosetta.rosetta.core.select.residue_selector) or_double_lazy_ig() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) or_ex1() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex1_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex1aro() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex1aro_exposed() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex1aro_exposed_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex1aro_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex2() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex2_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex2aro() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex2aro_exposed() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex2aro_exposed_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex2aro_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex3() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex3_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex4() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex4_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_exdna_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_fix_his_tautomer() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_flip_HNQ() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_include_current() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_include_virtual_side_chain() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_lazy_ig() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) or_linmem_ig() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) or_multi_cool_annealer() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) or_operate_on_ex1() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_operate_on_ex2() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_operate_on_ex3() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_operate_on_ex4() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_optimize_h() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method)

or_optimize_h_mode() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) or_preserve_c_beta() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_randomize2() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) Orbital (class in pyrosetta.rosetta.core.chemical) orbital() (pyrosetta.rosetta.core.chemical.ResidueType method) orbital_icoor_data() (pyrosetta.rosetta.core.chemical.ResidueType method) orbital_index() (pyrosetta.rosetta.core.chemical.ResidueType method) orbital_name() (pyrosetta.rosetta.core.conformation.Residue method) orbital_type() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) orbital_type_enum (class in pyrosetta.rosetta.core.chemical.orbitals) orbital_type_index() (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.conformation.Residue method) orbital_type_set() (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) orbital_types_ptr() (pyrosetta.rosetta.core.chemical.ResidueType method) orbital_xyz() (pyrosetta.rosetta.core.conformation.Residue method) OrbitalsFeaturesCreator (class in pyrosetta.rosetta.protocols.features) order() (in module pyrosetta.rosetta.protocols.forge.methods) (pyrosetta.rosetta.core.chemical.Bond method) order_by_energy() (pyrosetta.rosetta.core.io.silent.SilentFileData method) ordered_constrained_positions() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) ordered_pt_wat_penalty() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) ordered_wat_penalty() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) orient() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) orient_onto_residue() (pyrosetta.rosetta.core.conformation.Residue method) orient_onto_residue_peptoid() (pyrosetta.rosetta.core.conformation.Residue method) orient_residue_for_ideal_bond() (in module pyrosetta.rosetta.core.conformation) orient_rotamer_set_to_symmetric_partner() (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) orient_rotamer_to_symmetric_partner() (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) Orientation (class in pyrosetta.rosetta.core.conformation.membrane) orientations() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) orig_rotamer_id_for_moltenres() (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) original2modified() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) original2modified_interval_endpoints() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) original_deleted_positions() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) original_end() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) original_fixed_positions() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) original_interval() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) original_interval_valid() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) original_kept_positions() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) original_mutable_positions() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) original_pose_residue_is_in_residue_map() (in module pyrosetta.rosetta.protocols.generalized_kinematic_closure) original_sequence() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) originating_node_MPI_rank() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) OrJumpSelector (class in pyrosetta.rosetta.core.select.jump_selector) OrResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) OrSelector (class in pyrosetta.rosetta.protocols.pose_selectors) orstream (class in pyrosetta.rosetta.utility.io) ortho_check() (pyrosetta.rosetta.core.kinematics.Jump method) other_atom() (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) other_helix() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) other_pose() (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) other_pose_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) other_struct_list() (pyrosetta.rosetta.core.io.silent.SilentStruct method) out_of_bounds_memory_access() (in module pyrosetta.rosetta.protocols.toolbox) outer_product() (in module pyrosetta.rosetta.numeric) outgoing_message_queue_is_empty() (pyrosetta.rosetta.utility.SimulateMPI method) output_all_tag_options() (in module pyrosetta.rosetta.utility.xsd_util) output_alternate_atomids() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) output_alternative_states() (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) output_base_pairs() (in module pyrosetta.rosetta.core.pose.rna) output_base_stacks() (in module pyrosetta.rosetta.core.pose.rna) output_bool_list() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) output_boolean() (in module pyrosetta.rosetta.core.pose.rna) (in module pyrosetta.rosetta.protocols.stepwise.modeler) output_callback() (pyrosetta.rosetta.basic.PyTracer method) output_cluster_size() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) output_connectivity() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) output_constraints_file() (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) output_count() (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) output_data() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) output_debug_structure() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) output_dimacs() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) output_etable() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) output_fasta_file() (in module pyrosetta.rosetta.core.sequence) output_file_name() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) output_fold_tree_info() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) output_fragments() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) output_index() (pyrosetta.rosetta.protocols.jd3.output.OutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification method) output_intermediate_pose() (in module pyrosetta.rosetta.protocols.jd2) output_is_prepend_map() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) output_min_pose() (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) output_minimized_pose_list() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) output_motifs_to_pymol() (in module pyrosetta.rosetta.core.scoring.rna) output_movemap() (in module pyrosetta.rosetta.protocols.stepwise.modeler) output_name() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) Output_options (class in pyrosetta.rosetta.utility.json_spirit) output_other_contacts() (in module pyrosetta.rosetta.core.pose.rna) output_packstat() (in module pyrosetta.rosetta.protocols.vip) output_packstat_pdb() (in module pyrosetta.rosetta.core.scoring.packstat) output_pair_size() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) output_pose_cache() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) output_pose_energies_table() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) output_pose_list() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) output_prefix() (pyrosetta.rosetta.basic.TracerImpl method) output_res_map() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) output_results() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) output_rna_motif() (in module pyrosetta.rosetta.core.scoring.rna) output_rna_motifs() (in module pyrosetta.rosetta.core.scoring.rna) output_rna_motifs_detailed() (in module pyrosetta.rosetta.core.scoring.rna) output_scorefile() (in module pyrosetta) output_secondary_structure() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) output_seq_num_list() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) output_silent() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) output_silent_file() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) output_silent_struct() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) output_size_list() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) output_sqc_file() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) output_stems() (in module pyrosetta.rosetta.core.pose.rna) output_string_real_pairs_begin() (pyrosetta.rosetta.protocols.jd2.Job method) output_string_real_pairs_end() (pyrosetta.rosetta.protocols.jd2.Job method) output_string_string_pairs_begin() (pyrosetta.rosetta.protocols.jd2.Job method) output_string_string_pairs_end() (pyrosetta.rosetta.protocols.jd2.Job method) output_strings_begin() (pyrosetta.rosetta.protocols.jd2.Job method) output_strings_end() (pyrosetta.rosetta.protocols.jd2.Job method) output_tag() (pyrosetta.rosetta.protocols.jobdist.BasicJob method) output_title_text() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) output_to_silent_file() (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) output_torsions() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) output_type() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) output_virtual() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) output_virtual_zero_occ() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) OutputLevel (class in pyrosetta.rosetta.protocols.rotamer_recovery) OutputSpecification (class in pyrosetta.rosetta.protocols.jd3.output) outputter() (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) outputter_for_job() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter method) outputter_type() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification method) overall_constraints_strength() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) overall_energy0() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) overall_Ktheta() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) overall_max_count() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) overall_theta0() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) overlap() (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) overlap_chainbreak() (in module pyrosetta.rosetta.protocols.forge.methods) overlapping_with_region() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) overlaps() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) overlay() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) OversaturatedHbondAcceptorFilter (class in pyrosetta.rosetta.protocols.cyclic_peptide) owner_nodes_and_locations() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) ozstream (class in pyrosetta.rosetta.utility.io)

P

p1_deriv() (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) p1_theta_deriv() (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) p2_deriv() (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) p_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) P_omega0() (in module pyrosetta.rosetta.numeric.crick_equations) pack_all_side_chains() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) pack_and_minimize_linker_and_sidechains() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) pack_missing_sidechains() (in module pyrosetta.rosetta.core.pack) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) pack_o2prime_hydrogens() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) pack_polar_hydrogens() (in module pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens) pack_protein_side_chains() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) pack_residue() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) pack_rotamers() (in module pyrosetta.rosetta.core.pack) pack_rotamers_cleanup() (in module pyrosetta.rosetta.core.pack) pack_rotamers_loop() (in module pyrosetta.rosetta.core.pack) pack_rotamers_run() (in module pyrosetta.rosetta.core.pack) pack_rotamers_setup() (in module pyrosetta.rosetta.core.pack) pack_scorefxn_pose_handshake() (in module pyrosetta.rosetta.core.pack) pack_temp() (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) pack_weights() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) packed_residues() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) PackerEnergyAdd() (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) PackerEnergyMultiply() (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) PackerEnergySubtract() (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) PackerNeighborGraphFilter (class in pyrosetta.rosetta.protocols.simple_filters) PackerTask (class in pyrosetta.rosetta.core.pack.task) packertask() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) PackerTask_ (class in pyrosetta.rosetta.core.pack.task) PackerTaskSymmetryStatus (class in pyrosetta.rosetta.core.pack.task) packing_angle_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) packing_angle_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) PackingAngleEnum (class in pyrosetta.rosetta.protocols.antibody) PackPwatRotamersMover (class in pyrosetta.rosetta.protocols.simple_moves) PackRotamersMover (class in pyrosetta.rosetta.protocols.minimization_packing) PackRotamersMoverLazy (class in pyrosetta.rosetta.protocols.minimization_packing) PackRotamersMoverPartGreedy (class in pyrosetta.rosetta.protocols.enzdes) pad() (in module pyrosetta.rosetta.ObjexxFCL) pad_left() (in module pyrosetta.rosetta.utility) pad_results() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) pad_right() (in module pyrosetta.rosetta.utility) padded() (in module pyrosetta.rosetta.ObjexxFCL) pair_energy_H_v() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) pair_has_linkage_statistics() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) pair_sets_with_positions() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) paired() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) PairedSheetResidueSelector (class in pyrosetta.rosetta.protocols.denovo_design.residue_selectors) PairFeaturesCreator (class in pyrosetta.rosetta.protocols.features) pairing_group_namer() (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) pairing_subelement_ct_namer() (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) PalesEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) parallel_base_test() (in module pyrosetta.rosetta.protocols.motifs) ParallelTempering (class in pyrosetta.rosetta.protocols.canonical_sampling) ParallelTemperingCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) param_cache() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) param_index() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) Parameters (class in pyrosetta.rosetta.core.conformation.parametric) parameters() (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) parameters_for_restype() (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) parameters_set() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) ParametersSet (class in pyrosetta.rosetta.core.conformation.parametric) paratope_charge() (in module pyrosetta.rosetta.protocols.antibody) paratope_sasa() (in module pyrosetta.rosetta.protocols.antibody) ParatopeEpitopeSiteConstraintMover (class in pyrosetta.rosetta.protocols.antibody.constraints) ParatopeSiteConstraintMover (class in pyrosetta.rosetta.protocols.antibody.constraints) parent() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.utility.file.PathName method) parent_node() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) parin_favorite_output() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) parse() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) parse_adduct_string() (in module pyrosetta.rosetta.core.chemical) parse_atom_pair_constraint() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) parse_atom_type_data() (in module pyrosetta.rosetta.core.chemical.sdf) parse_attributes_from_tag() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) parse_command_line() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) parse_constraint_generators() (in module pyrosetta.rosetta.protocols.constraint_generator) parse_coordinate_constraint() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) parse_custom_torsion() (in module pyrosetta.rosetta.protocols.constraint_generator) parse_database_connection() (in module pyrosetta.rosetta.basic.database) parse_database_session() (in module pyrosetta.rosetta.protocols.rosetta_scripts) parse_default_and_user_options() (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser method) parse_dof_task_type() (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) parse_dof_tasks() (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) parse_elazar_polynom_table() (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) parse_elazar_spline_table() (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) parse_energies() (pyrosetta.rosetta.core.io.silent.SilentStruct method) parse_excluded_properites() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) parse_excluded_types() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) parse_filter() (in module pyrosetta.rosetta.protocols.rosetta_scripts) parse_grid_set_from_tag() (in module pyrosetta.rosetta.protocols.qsar.scoring_grid) parse_gridset_tag() (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) parse_in_progress() (pyrosetta.rosetta.core.io.HeaderInformation method) parse_included_properites() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) parse_included_types() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) parse_jump_selector() (in module pyrosetta.rosetta.core.select.jump_selector) parse_length_string() (in module pyrosetta.rosetta.protocols.denovo_design) parse_lengths() (in module pyrosetta.rosetta.protocols.denovo_design.components) parse_loops_from_tag() (in module pyrosetta.rosetta.protocols.loop_modeling.utilities) parse_motif() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) parse_motif_string() (in module pyrosetta.rosetta.protocols.denovo_design) parse_movemap_factory() (in module pyrosetta.rosetta.core.select.movemap) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) parse_movemap_factory_legacy() (in module pyrosetta.rosetta.protocols.rosetta_scripts) parse_mover() (in module pyrosetta.rosetta.protocols.rosetta_scripts) parse_my_tag() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.TotalEnergyMetric method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) parse_named_movemap_factory_legacy() (in module pyrosetta.rosetta.protocols.rosetta_scripts) parse_NMR_name() (in module pyrosetta.rosetta.core.scoring.constraints) parse_optional_grid_set_from_tag() (in module pyrosetta.rosetta.protocols.qsar.scoring_grid) parse_options() (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser method) parse_opts() (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) parse_or_properties() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) parse_orientations() (in module pyrosetta.rosetta.protocols.denovo_design.components) parse_out_non_standard_residues() (in module pyrosetta.rosetta.core.sequence) parse_PDBnum_icode() (in module pyrosetta.rosetta.core.pose) parse_plain_text_with_columns() (in module pyrosetta.rosetta.protocols.antibody.grafting) parse_protocol_tag() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) parse_quota_command_line() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) parse_report_format_string() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) parse_res_agnostic_commands() (in module pyrosetta.rosetta.core.pack.task) parse_resfile() (in module pyrosetta.rosetta.core.pack.task) parse_resfile_string() (in module pyrosetta.rosetta.core.pack.task) parse_resfile_string_with_no_lockdown() (in module pyrosetta.rosetta.protocols.forge.methods) parse_residue() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) parse_residue_level_task_operations() (in module pyrosetta.rosetta.core.pack.task.operation) parse_residue_selector() (in module pyrosetta.rosetta.core.select.residue_selector) parse_residue_selector_logic_string() (in module pyrosetta.rosetta.core.select.residue_selector) parse_resnames() (in module pyrosetta.rosetta.protocols.helical_bundle) parse_resnum() (in module pyrosetta.rosetta.core.pose) parse_rotamer_sampling_data() (in module pyrosetta.rosetta.core.pack.task.operation) parse_score_function() (in module pyrosetta.rosetta.core.scoring) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) parse_seeds() (in module pyrosetta.rosetta.protocols.seeded_abinitio) parse_segment_names() (in module pyrosetta.rosetta.protocols.denovo_design.connection) parse_sequence() (in module pyrosetta.rosetta.core.pose) parse_string_to_boolean_expression() (in module pyrosetta.rosetta.numeric.expression_parser) parse_string_to_expression() (in module pyrosetta.rosetta.numeric.expression_parser) parse_string_to_residue_selector() (pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser method) parse_stub_sets() (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) parse_tag() (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation method) parse_task_operations() (in module pyrosetta.rosetta.core.pack.task) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) parse_torsion_type() (in module pyrosetta.rosetta.protocols.constraint_generator) parse_xyz_vector() (in module pyrosetta.rosetta.protocols.rosetta_scripts) partial_align() (in module pyrosetta.rosetta.protocols.hybridization) PartialSecondarySimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) Particle (class in pyrosetta.rosetta.core.optimization) ParticleSwarmMinimizer (class in pyrosetta.rosetta.core.optimization) partition_by_jump() (pyrosetta.rosetta.core.kinematics.FoldTree method) partition_by_residue() (pyrosetta.rosetta.core.kinematics.FoldTree method) partition_by_symm_jumps() (in module pyrosetta.rosetta.core.pose.symmetry) partition_coloring() (pyrosetta.rosetta.core.kinematics.FoldTree method) partition_definition() (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) partition_pose_by_jump() (in module pyrosetta.rosetta.core.pose) Partner (class in pyrosetta.rosetta.protocols.rigid) partner() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) partner1() (pyrosetta.rosetta.protocols.contact_map.Contact method) partner2() (pyrosetta.rosetta.protocols.contact_map.Contact method) partners() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) pass_metropolis() (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) passes_com_vector_criterion() (pyrosetta.rosetta.protocols.match.NumNeighborsMPM method) passes_filter() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) passes_filters() (in module pyrosetta.rosetta.protocols.ligand_docking) passes_hardsphere_filter() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) Patch (class in pyrosetta.rosetta.core.chemical) patch_map() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) patch_name_from_affix() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) patch_operation_from_patch_file_line() (in module pyrosetta.rosetta.core.chemical) PatchCase (class in pyrosetta.rosetta.core.chemical) PatchdockTransform (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) patched_name() (pyrosetta.rosetta.core.chemical.Patch method) patches() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) PatchOperation (class in pyrosetta.rosetta.core.chemical) path() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) path_basename() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) path_dist() (pyrosetta.rosetta.core.scoring.AtomNeighbor method) path_distance() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) path_distances() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) PathName (class in pyrosetta.rosetta.utility.file) pathname() (in module pyrosetta.rosetta.utility) PathOption (class in pyrosetta.rosetta.utility.options) PathOptionKey (class in pyrosetta.rosetta.utility.options) PathVectorOption (class in pyrosetta.rosetta.utility.options) PathVectorOptionKey (class in pyrosetta.rosetta.utility.options) pb_bound_tag() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) pb_unbound_tag() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) pbest() (pyrosetta.rosetta.core.optimization.Particle method) PBP_clustering_at_chain_closure() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) PCluster (class in pyrosetta.rosetta.protocols.pockets) PClusterSet (class in pyrosetta.rosetta.protocols.pockets) PCS_data_input (class in pyrosetta.rosetta.protocols.scoring.methods.pcs) PCS_data_input_Ts1 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) PCS_data_input_Ts2 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) PCS_data_input_Ts3 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) PCS_data_input_Ts4 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) PCS_experimental() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) PCS_file_data (class in pyrosetta.rosetta.protocols.scoring.methods.pcs) PCS_file_data_Ts1 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) PCS_file_data_Ts2 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) PCS_file_data_Ts3 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) PCS_file_data_Ts4 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) PCS_FragDistance (class in pyrosetta.rosetta.protocols.frag_picker.scores) PCS_line_data (class in pyrosetta.rosetta.protocols.scoring.methods.pcs) PCS_line_data_Ts1 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) PCS_line_data_Ts2 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) PCS_line_data_Ts3 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) PCS_line_data_Ts4 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) PCS_tolerance() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) PcsInputCenter (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) PcsInputFile (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) PcsInputLine (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) pd_reader() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) PDatom (class in pyrosetta.rosetta.core.scoring) pdb2pose() (pyrosetta.rosetta.core.pose.PDBInfo method) pdb_code_from_rosetta_name() (pyrosetta.rosetta.core.io.NomenclatureManager method) pdb_comments() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileRep method) pdb_count() (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) pdb_end() (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) pdb_info() (pyrosetta.rosetta.core.pose.Pose method) pdb_parents() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) pdb_start() (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) pdb_to_pose() (in module pyrosetta.rosetta.core.pose) PdbDataFeaturesCreator (class in pyrosetta.rosetta.protocols.features) pdbid() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) PDBInfo (class in pyrosetta.rosetta.core.pose) PDBJobInputter (class in pyrosetta.rosetta.protocols.jd2) PDBJobOutputter (class in pyrosetta.rosetta.protocols.jd2) PDBLandmark (class in pyrosetta.rosetta.protocols.antibody) PDBNumbering (class in pyrosetta.rosetta.protocols.antibody.design) pdbpos() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) PDBPoseMap (class in pyrosetta.rosetta.core.pose) PDBSilentStructCreator (class in pyrosetta.rosetta.core.import_pose) pdbslice() (in module pyrosetta.rosetta.core.pose) (in module pyrosetta.rosetta.protocols.magnesium) PDBTrajectoryRecorder (class in pyrosetta.rosetta.protocols.canonical_sampling) PDBTrajectoryRecorderCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) PDinter (class in pyrosetta.rosetta.core.scoring.power_diagram) PDsphere (class in pyrosetta.rosetta.core.scoring.power_diagram) PDvertex (class in pyrosetta.rosetta.core.scoring.power_diagram) peak_volume() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) PeakAssignment (class in pyrosetta.rosetta.protocols.noesy_assign) PeakAssignmentResidueMap (class in pyrosetta.rosetta.protocols.noesy_assign) peek() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) penalty() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup method) peptide_entry() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) peptide_length() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) PeptideDeriverBasicStreamOutputter (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverEntryType (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverFilter (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverMarkdownStreamOutputter (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverOutputter (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverOutputterContainer (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverPoseOutputter (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverReportFormat (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideStapleDesignMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) per_chain_renumbering() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) per_res_sc_sasa() (in module pyrosetta.rosetta.core.scoring.sasa) percent_native() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) perform_all_reactions() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) perform_major_reaction_only() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) performing_pure_insertion() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) performs_major_reaction_only() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) periodic_range() (in module pyrosetta.rosetta.basic) PeriodicBoundFunc (class in pyrosetta.rosetta.core.scoring.constraints) PeriodicFunc (class in pyrosetta.rosetta.core.scoring.func) periodicity() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) PerResidueInterfaceData (class in pyrosetta.rosetta.protocols.analysis) pert() (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) pert_size() (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) PertMinMover (class in pyrosetta.rosetta.protocols.minimization_packing) PertType (class in pyrosetta.rosetta.protocols.helical_bundle) perturb() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) perturb_angles() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_backbone_for_test() (in module pyrosetta.rosetta.protocols.grafting) perturb_beta_residue() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) perturb_c_n() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_c_n_ca() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_ca_c() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_ca_c_n() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_chain() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) perturb_lengths() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_n_ca() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_n_ca_c() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_omega() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_phi() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_psi() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_sequence() (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) perturb_subset() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) perturb_subset_with_balance() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) perturb_torsions() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_weights() (pyrosetta.rosetta.core.scoring.ScoreFunction method) perturb_with_balance() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) perturbation_magnitude() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) perturbation_type() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) PerturbBundleOptions (class in pyrosetta.rosetta.protocols.helical_bundle) PerturbByBins (class in pyrosetta.rosetta.protocols.simple_moves.bin_transitions) PerturbChiSidechainMover (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) perturbed_sequence() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) Perturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) perturber() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) perturber_effect (class in pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber) perturber_exhausted() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) perturber_type() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) PerturberSet (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) PerturbRotamerSidechainMover (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) pH_mode_exceptions() (in module pyrosetta.rosetta.core.chemical) phe_tyr_corrections() (in module pyrosetta.rosetta.protocols.make_rot_lib) Phi (class in pyrosetta.rosetta.protocols.frag_picker.scores) phi() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) phi_max() (pyrosetta.rosetta.core.sequence.ABEGO method) phi_min() (pyrosetta.rosetta.core.sequence.ABEGO method) PhiPsiRmsd (class in pyrosetta.rosetta.protocols.frag_picker.scores) PhiPsiSquareWell (class in pyrosetta.rosetta.protocols.frag_picker.scores) PhiSelector (class in pyrosetta.rosetta.core.select.residue_selector) phosphate_base_phosphate_rmsd() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) phosphate_base_phosphate_square_deviation() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) phosphate_square_deviation() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) PhosphateMover (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) PhosphateTerminus (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) pick() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots method) pick_and_apply() (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker method) pick_and_cache_fragments() (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) pick_candidates() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) pick_chunk_candidates() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) pick_fragments() (in module pyrosetta.rosetta.core.fragment.picking_old.vall) pick_fragments_by_ss() (in module pyrosetta.rosetta.core.fragment.picking_old.vall) pick_fragments_by_ss_plus_aa() (in module pyrosetta.rosetta.core.fragment.picking_old.vall) pick_loops_chainbreak() (in module pyrosetta.rosetta.protocols.comparative_modeling) pick_loops_unaligned() (in module pyrosetta.rosetta.protocols.comparative_modeling) pick_loopy_cutpoint() (in module pyrosetta.rosetta.core.kinematics) pick_new_cutpoints() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) pick_sequence_from_database() (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) pick_solution() (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) Picker (class in pyrosetta.rosetta.protocols.denovo_design.components) picking_rounds() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) PIKAA (class in pyrosetta.rosetta.core.pack.task) PIKNA (class in pyrosetta.rosetta.core.pack.task) PIKRNA (class in pyrosetta.rosetta.core.pack.task) pivot1() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) pivot2() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) pivot_atoms() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) pivot_loop() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) pivot_residues() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) PivotPicker (class in pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers) place() (pyrosetta.rosetta.core.conformation.Residue method) place_atom_positions() (in module pyrosetta.rosetta.protocols.helical_bundle) place_de_novo_wat_at_anchor() (in module pyrosetta.rosetta.protocols.hydrate) place_stubs() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) placeholder_clone() (pyrosetta.rosetta.core.chemical.ResidueType method) placeholder_info() (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) placeholder_residue() (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) PlacementMinimizationMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) PlaceSimultaneouslyMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) PlaceStubMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) PlainPdbJobDistributor (class in pyrosetta.rosetta.protocols.jobdist) PlainRawJobDistributor (class in pyrosetta.rosetta.protocols.jobdist) PlainSilentFileJobDistributor (class in pyrosetta.rosetta.protocols.jobdist) plus_plus() (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.protocols.match.VoxelSetIterator method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator method) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.EdgeListIterator method) pmatch() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) PocketConstraint (class in pyrosetta.rosetta.protocols.pockets) PocketConstraintCreator (class in pyrosetta.rosetta.protocols.pockets) PocketExemplarMultifunc (class in pyrosetta.rosetta.protocols.pockets) PocketGrid (class in pyrosetta.rosetta.protocols.pockets) point_for_nonchitip_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) point_on_ellipsoid() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) points_for_nonchitip_atoms() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) POLAR (class in pyrosetta.rosetta.core.pack.task) polar_sc_atoms_not_satisfied_by_background() (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) PolarGroupBurialPyMolStringMetric (class in pyrosetta.rosetta.protocols.analysis.burial_metrics) PolarHydrogenFilter (class in pyrosetta.rosetta.core.chemical) Policy (class in pyrosetta.rosetta.protocols.nonlocal) polycubic_interpolation() (in module pyrosetta.rosetta.core.pack.dunbrack) polymer_direction() (pyrosetta.rosetta.core.kinematics.Edge method) PolymerBondedEnergyContainer (class in pyrosetta.rosetta.core.scoring) PolymerBondedNeighborConstIterator (class in pyrosetta.rosetta.core.scoring) PolymerBondedNeighborIterator (class in pyrosetta.rosetta.core.scoring) polymeric_oriented_sequence_distance() (pyrosetta.rosetta.core.conformation.Residue method) polymeric_sequence_distance() (pyrosetta.rosetta.core.conformation.Residue method) polynom_by_z() (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) PoolEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) pop() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) pop_back() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) pop_passport() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) populate_all_cdrs() (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) populate_results_from_db() (in module pyrosetta.rosetta.protocols.antibody.grafting) pos() (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) pos_in_history_queue() (pyrosetta.rosetta.utility.recent_history_queue method) pos_mod() (in module pyrosetta.rosetta.core.scoring.electron_density) (in module pyrosetta.rosetta.protocols.cryst) Pose (class in pyrosetta.rosetta.core.pose) pose() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) pose1_has_most_CBs() (in module pyrosetta.rosetta.protocols.sic_dock) pose2pdb() (pyrosetta.rosetta.core.pose.PDBInfo method) pose_aligner() (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) pose_cache_float_data() (pyrosetta.rosetta.core.io.StructFileRep method) pose_cache_string_data() (pyrosetta.rosetta.core.io.StructFileRep method) pose_charge() (in module pyrosetta.rosetta.protocols.antibody) pose_cop() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) pose_data_cache_from_sfr() (in module pyrosetta.rosetta.core.io) pose_energies_from_sfr() (in module pyrosetta.rosetta.core.io) pose_energies_to_json() (in module pyrosetta.rosetta.protocols.rpc) pose_energy() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) pose_from_atom_tree_diff() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) pose_from_file() (in module pyrosetta.rosetta.core.import_pose) pose_from_job() (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) pose_from_pdb_stream() (in module pyrosetta.rosetta.core.import_pose) pose_from_pdbstring() (in module pyrosetta.rosetta.core.import_pose) pose_from_pose() (in module pyrosetta.rosetta.core.io) pose_from_rcsb() (in module pyrosetta.toolbox.rcsb) pose_from_saccharide_sequence() (in module pyrosetta.rosetta.core.pose) pose_from_sequence() (in module pyrosetta.io) (in module pyrosetta.toolbox.mutants) pose_has_nonzero_Bs() (in module pyrosetta.rosetta.core.scoring.electron_density) pose_index() (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) pose_input_stream() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) pose_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) pose_loop_anchors() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) pose_matches_user_tag() (in module pyrosetta.rosetta.protocols.jobdist) pose_max_nbr_radius() (in module pyrosetta.rosetta.core.pose) pose_num() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) pose_numbered() (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) pose_raw_unfolded_state_energymap() (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential method) pose_residue_is_terminal() (in module pyrosetta.rosetta.core.pose) pose_right() (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) pose_seq() (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) pose_setup_from_file() (in module pyrosetta.rosetta.protocols.recces) pose_setup_turner() (in module pyrosetta.rosetta.protocols.recces) pose_tilt_angle_and_center_distance() (in module pyrosetta.rosetta.protocols.membrane) pose_tm_com() (in module pyrosetta.rosetta.protocols.membrane) pose_to_pack_data() (in module pyrosetta.rosetta.core.scoring.packstat) pose_to_pdb() (in module pyrosetta.rosetta.core.pose) pose_to_segment() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) pose_with_most_CBs() (in module pyrosetta.rosetta.protocols.sic_dock) PoseArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) poseBfacts2multivec() (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) PoseComment (class in pyrosetta.rosetta.protocols.simple_filters) PoseCommentsFeaturesCreator (class in pyrosetta.rosetta.protocols.features) PoseConformationFeaturesCreator (class in pyrosetta.rosetta.protocols.features) PoseCoordPickMode (class in pyrosetta.rosetta.core.pose) PoseFolder (class in pyrosetta.rosetta.protocols.denovo_design.components) PoseForPoseID (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts) PoseFoundResiduesCombination (class in pyrosetta.rosetta.protocols.enzdes) PoseFromPoseResourceMover (class in pyrosetta.rosetta.protocols.simple_moves) PoseFromSFRBuilder (class in pyrosetta.rosetta.core.io.pose_from_sfr) PoseInfoFilter (class in pyrosetta.rosetta.protocols.simple_filters) PoseInputStreamJobInputter (class in pyrosetta.rosetta.protocols.jd2) PoseInputter (class in pyrosetta.rosetta.protocols.jd3.pose_inputters) PoseMatchOutputWriter (class in pyrosetta.rosetta.protocols.match.output) PoseMetricContainer (class in pyrosetta.rosetta.core.pose.metrics) PoseNumberedLoopFileReader (class in pyrosetta.rosetta.protocols.loops) poseOPs_from_files() (in module pyrosetta.rosetta.core.import_pose) PoseOutputSpecification (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) PoseOutputter (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) PosePropertyReporterCreator (class in pyrosetta.rosetta.protocols.rosetta_scripts) PoseResidueAccessor (class in pyrosetta.bindings.pose) PoseResidueTypeSet (class in pyrosetta.rosetta.core.chemical) poses_from_cmd_line() (in module pyrosetta.rosetta.protocols.comparative_modeling) poses_from_files() (in module pyrosetta.rosetta.core.import_pose) poses_from_silent() (in module pyrosetta.io) PoseSelectorCreator (class in pyrosetta.rosetta.protocols.rosetta_scripts) PoseSelectorFlags (class in pyrosetta.rosetta.protocols.rosetta_scripts) poseSphericalSamples() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) PoseToStructFileRepConverter (class in pyrosetta.rosetta.core.io.pose_to_sfr) position() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) position_ala_ddG() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) position_cutpoint_phosphate_torsions() (in module pyrosetta.rosetta.core.pose.rna) position_data_begin() (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) position_data_end() (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) position_five_prime_phosphate() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) position_index() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) position_of_atom_on_ring() (in module pyrosetta.rosetta.core.conformation) position_untouchable() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) PositionConservedResiduesStore (class in pyrosetta.rosetta.core.pose.datacache) PositionDdGInfo (class in pyrosetta.rosetta.core.io.PositionDdGInfo) positions() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) positions_in_secstruct() (in module pyrosetta.rosetta.protocols.simple_filters) positions_incompatible_with_task() (in module pyrosetta.rosetta.protocols.backrub) PositionSpecificRandomizer (class in pyrosetta.rosetta.protocols.genetic_algorithm) PositionType (class in pyrosetta.rosetta.protocols.dna) positive() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) positive_pow() (in module pyrosetta.rosetta.core.pack.dunbrack) positive_value() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) possible_root() (in module pyrosetta.rosetta.protocols.rna.denovo) (pyrosetta.rosetta.core.kinematics.FoldTree method) PossibleAtomTypesForAtom (class in pyrosetta.rosetta.core.chemical.gasteiger) possibly_canonical() (in module pyrosetta.rosetta.core.chemical.rna) possibly_canonical_strict() (in module pyrosetta.rosetta.core.chemical.rna) post_catalog_op() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) post_relax_round_update_steps() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) pow() (in module pyrosetta.rosetta.ObjexxFCL) power() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) power_distance() (in module pyrosetta.rosetta.core.scoring.power_diagram) PowerDiagram (class in pyrosetta.rosetta.core.scoring.power_diagram) PP() (in module pyrosetta.rosetta.numeric.crick_equations) ppo_torsion_bin (class in pyrosetta.rosetta.core.conformation) PQR (class in pyrosetta.rosetta.core.scoring) pre_catalog_op() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) pre_chitip_transform() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) pre_load_data() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) pre_process() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) pre_relax_round_update_steps() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) pre_tracer_process() (in module pyrosetta.rosetta.basic.options) preallocate() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) preamble() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) preapply() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) precision() (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) precompute_transforms() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) predefine_search() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) Predicate (class in pyrosetta.rosetta.core.scoring) PredictedBurialFnEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) preexisting_positions() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) preferred_root_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) prefix() (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.utility.options.OptionCollection method) preload_motif_data() (in module pyrosetta.rosetta.core.scoring.motif) prepack() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) prepare_for_match_enumeration() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) prepare_for_output() (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement method) prepare_for_output_writing() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) prepare_for_packing() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) prepare_for_simulated_annealing() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) prepare_pose() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) prepare_rotamers_for_packing() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) prepare_scoring() (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) prepare_scratch_residue() (in module pyrosetta.rosetta.core.pose.rna) prepare_silent_struct() (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo) prepare_statement_no_catch() (in module pyrosetta.rosetta.basic.database) prepare_to_note_hits_for_completed_round() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) PrepareForCentroid (class in pyrosetta.rosetta.protocols.loop_modeling.utilities) PrepareForFullatom (class in pyrosetta.rosetta.protocols.loop_modeling.utilities) prepend_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) prepend_new_residues() (in module pyrosetta.rosetta.protocols.denovo_design.components) prepend_output_name() (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) prepend_polymer_residue_before_seqpos() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) prepend_res() (pyrosetta.rosetta.core.pose.PDBInfo method) PrependMainchainAtom (class in pyrosetta.rosetta.core.chemical) preprocess_data() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) preserve_atom_coords() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) preserve_c_beta() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) preserve_crystinfo() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) preserve_detailed_balance() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method)

preserve_header() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) pretty() (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter method) pretty_print_atomicoor() (in module pyrosetta.rosetta.core.chemical) pretty_print_rd() (in module pyrosetta.rosetta.protocols.make_rot_lib) prevent_repacking() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation method) PreventChainFromRepackingOperation (class in pyrosetta.rosetta.protocols.task_operations) PreventRepacking (class in pyrosetta.rosetta.core.pack.task.operation) PreventResiduesFromRepackingOperation (class in pyrosetta.rosetta.protocols.task_operations) previous() (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) previous_child() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) previous_round_geometry_still_matchable() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) previous_sibling() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) previous_working_pack_res() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) PrimarySequenceNeighborhoodSelector (class in pyrosetta.rosetta.core.select.residue_selector) principal_angle_degrees() (in module pyrosetta.rosetta.numeric) principal_components_and_eigenvalues_ndimensions() (in module pyrosetta.rosetta.numeric) PrincipalQuantumNumber_strings() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) print() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.Bond method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) print_all_bond_lengths() (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) print_all_types() (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) print_allowed_types() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) print_atom_pair_constraints() (in module pyrosetta.rosetta.core.scoring.constraints) print_atom_pair_energy_table() (in module pyrosetta) print_backbone_torsions() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) print_base_centroid_atoms_for_rb_entropy() (in module pyrosetta.rosetta.protocols.recces) print_base_state() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) print_bondangles() (pyrosetta.rosetta.core.chemical.ResidueType method) print_chis() (in module pyrosetta.rosetta.core.chemical) print_comments() (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_conformation() (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_current_state_assignment() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) print_debug() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) print_dihedrals() (pyrosetta.rosetta.core.chemical.ResidueType method) print_dofs() (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) print_fragment() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) print_fragment_index() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) print_fragment_seq() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) print_generators() (in module pyrosetta.rosetta.core.scoring.power_diagram) print_hbonds() (in module pyrosetta.rosetta.protocols.rna.denovo) print_header() (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_headers() (in module pyrosetta.rosetta.protocols.hbnet) print_information() (in module pyrosetta.rosetta.protocols.rosetta_scripts) print_internal_coords() (in module pyrosetta.rosetta.protocols.rna.denovo) print_list_to_string() (in module pyrosetta.rosetta.protocols.hbnet) print_metric() (pyrosetta.rosetta.core.pose.Pose method) print_network() (in module pyrosetta.rosetta.protocols.hbnet) print_network_w_pdb_numbering() (in module pyrosetta.rosetta.protocols.hbnet) print_parent_remarks() (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_partners() (in module pyrosetta.rosetta.core.scoring.power_diagram) print_point() (in module pyrosetta.rosetta.numeric.kdtree) print_points() (in module pyrosetta.rosetta.numeric.kdtree) print_pretty_path_distances() (pyrosetta.rosetta.core.chemical.ResidueType method) print_probabilities() (in module pyrosetta.rosetta.numeric) print_report() (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) print_residue_numbers() (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_residue_pair_energies() (in module pyrosetta) print_residues_near_water() (in module pyrosetta.rosetta.protocols.hydrate) print_score() (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) print_score_header() (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_scores() (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_submotif_info() (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_sugar_pucker_state() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) print_template_script() (in module pyrosetta.rosetta.protocols.rosetta_scripts) print_torsion_info() (in module pyrosetta.rosetta.core.pose.rna) (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) print_tree() (in module pyrosetta.rosetta.numeric.kdtree) print_vertex_groups() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) print_vertices() (in module pyrosetta.rosetta.core.scoring.power_diagram) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) print_WorkingParameters_info() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) priority() (pyrosetta.rosetta.basic.TracerImpl method) private_data_to_public_array() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) private_index() (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) prob() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) prob_random_pert_current() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) prob_sum_of_gaussians() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) prob_uniform() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) prob_withinrot() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) probability() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) probability_limit() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) probe_radius_for_atom_type() (in module pyrosetta.rosetta.protocols.match) ProbeRadius (class in pyrosetta.rosetta.protocols.match) process() (in module pyrosetta.rosetta.basic.options) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) process_decoy() (in module pyrosetta.rosetta.protocols.features.strand_assembly) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) process_deletions() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) process_hit() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor method) process_input_file() (in module pyrosetta.rosetta.core.import_pose) process_insertions() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) process_matches() (pyrosetta.rosetta.protocols.match.Matcher method) process_symmdef_file() (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) product() (in module pyrosetta.rosetta.core.pack.dunbrack) (in module pyrosetta.rosetta.numeric) prof_reset() (in module pyrosetta.rosetta.basic) prof_show() (in module pyrosetta.rosetta.basic) prof_start_function_body() (in module pyrosetta.rosetta.basic) prof_stop_function_body() (in module pyrosetta.rosetta.basic) profile() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) profile_struct() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) ProfileScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) ProfileScoreBlosum62 (class in pyrosetta.rosetta.protocols.frag_picker.scores) ProfileScoreDistWeight (class in pyrosetta.rosetta.protocols.frag_picker.scores) ProfileScoreL1 (class in pyrosetta.rosetta.protocols.frag_picker.scores) ProfileScoreStructL1 (class in pyrosetta.rosetta.protocols.frag_picker.scores) ProfileScoreSubMatrix (class in pyrosetta.rosetta.protocols.frag_picker.scores) ProfTag (class in pyrosetta.rosetta.basic) ProgressBarObserver (class in pyrosetta.rosetta.protocols.canonical_sampling) ProgressBarObserverCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) projection_matrix() (in module pyrosetta.rosetta.numeric) projperp() (in module pyrosetta.rosetta.protocols.sic_dock) ProlinePhiScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) promote_sameresidue_child_of_jump_atom() (in module pyrosetta.rosetta.core.conformation) promote_sameresidue_nonjump_child() (pyrosetta.rosetta.core.kinematics.AtomTree method) properties() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.ResidueType method) properties_match_this() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) PROPERTY (class in pyrosetta.rosetta.core.pack.task) property() (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) property_from_string() (pyrosetta.rosetta.core.chemical.AtomPropertiesManager method) property_penalty() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) property_set_indices_matching_residue() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) proposal_density() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) proposed_since_last_batch() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) protein_atom_name_to_num() (in module pyrosetta.rosetta.core.scoring.rna) protein_dielectric() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) protein_interface_design() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) ProteinBackboneAtomAtomPairFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ProteinBackboneTorsionAngleFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ProteinBondGeometryFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ProteinInterfaceDesignOperation (class in pyrosetta.rosetta.protocols.task_operations) ProteinInterfaceMultiStateDesignMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) ProteinLigandInterfaceUpweighter (class in pyrosetta.rosetta.protocols.enzdes) ProteinResidueConformationFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ProteinRMSDFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ProteinRMSDNoSuperpositionFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ProteinSilentStruct_SinglePrecCreator (class in pyrosetta.rosetta.core.io.silent) ProteinSilentStructCreator (class in pyrosetta.rosetta.core.io.silent) ProteinTorsion (class in pyrosetta.rosetta.core.scoring) protocol_option_set() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) proton_chi_2_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) proton_chi_extra_samples() (pyrosetta.rosetta.core.chemical.ResidueType method) proton_chi_samples() (pyrosetta.rosetta.core.chemical.ResidueType method) proton_indices() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) proton_tolerance() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) ProtonResonance (class in pyrosetta.rosetta.protocols.noesy_assign) provide_attributes() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) provide_pymol_commands_to_show_groups() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) provide_stored_derivatives() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) provide_xml_schema() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator method) (pyrosetta.rosetta.core.fragment.FragmentSetLoader method) (pyrosetta.rosetta.core.fragment.FragmentSetLoaderCreator method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.TotalEnergyMetric method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator method) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator method) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator method) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.FilterCreator method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMoverCreator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalRequirementCreator method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraintCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraintCreator method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MoverCreator method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader method) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DatabaseSessionLoader method) (pyrosetta.rosetta.protocols.parser.FragSetLoader method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) (pyrosetta.rosetta.protocols.parser.ResLvlTaskOperationLoader method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader method) (pyrosetta.rosetta.protocols.parser.SimpleMetricLoader method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) ProxySentinel (class in pyrosetta.rosetta.ObjexxFCL.internal) prune_cavity_balls() (in module pyrosetta.rosetta.core.scoring.packstat) prune_hidden_cavity_balls() (in module pyrosetta.rosetta.core.scoring.packstat) prune_voxels_for_fixed_residues() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) psc_compare() (in module pyrosetta.rosetta.core.pack.dunbrack) pseudobonds() (pyrosetta.rosetta.core.conformation.Residue method) Psi (class in pyrosetta.rosetta.protocols.frag_picker.scores) psi() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) psi_max() (pyrosetta.rosetta.core.sequence.ABEGO method) psi_min() (pyrosetta.rosetta.core.sequence.ABEGO method) public_array_to_private_data() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) PuckerState (class in pyrosetta.rosetta.core.chemical.rna) push() (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) push_back() (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) push_back_and_finalize() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) push_front() (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) push_passport() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) push_to_front_of_history_queue() (pyrosetta.rosetta.utility.recent_history_queue method) put() (pyrosetta.logging_support.PythonLoggingSink method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.TracerImpl method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) put_in_cutpoint() (in module pyrosetta.rosetta.core.import_pose) put_intra_into_total() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) put_jump_stubs_intra_residue() (pyrosetta.rosetta.core.kinematics.FoldTree method) putback() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) PValuedFragmentScoreManager (class in pyrosetta.rosetta.protocols.frag_picker.scores) PyEnergyMethodRegistrator (class in pyrosetta.rosetta.core.scoring.methods) PyExitCallback (class in pyrosetta.rosetta.utility.py) PyReturnValuePolicyTest_DummyClassCOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_DummyClassOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_PoseCOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_PoseOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_ScoreFunctionCOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_ScoreFunctionCOP2() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_ScoreFunctionOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_SF_ReplicaCOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_SF_ReplicaOP() (in module pyrosetta.rosetta.protocols.toolbox) pyrosetta (module) pyrosetta.bindings (module) pyrosetta.bindings.pose (module) pyrosetta.bindings.utility (module) pyrosetta.io (module) pyrosetta.logging_support (module) pyrosetta.method_bindings (module) pyrosetta.method_bindings.pose (module) pyrosetta.rosetta (module) pyrosetta.rosetta.basic (module) pyrosetta.rosetta.basic.database (module) pyrosetta.rosetta.basic.database.insert_statement_generator (module) pyrosetta.rosetta.basic.database.schema_generator (module) pyrosetta.rosetta.basic.datacache (module) pyrosetta.rosetta.basic.gpu (module) pyrosetta.rosetta.basic.mpi (module) pyrosetta.rosetta.basic.options (module) pyrosetta.rosetta.basic.resource_manager (module) pyrosetta.rosetta.basic.resource_manager.locator (module) pyrosetta.rosetta.basic.sampling (module) pyrosetta.rosetta.basic.sampling.orientations (module) pyrosetta.rosetta.basic.svd (module) pyrosetta.rosetta.core (module) pyrosetta.rosetta.core.chemical (module) pyrosetta.rosetta.core.chemical.carbohydrates (module) pyrosetta.rosetta.core.chemical.element (module) pyrosetta.rosetta.core.chemical.gasteiger (module) pyrosetta.rosetta.core.chemical.mainchain_potential (module) pyrosetta.rosetta.core.chemical.mmCIF (module) pyrosetta.rosetta.core.chemical.NucleotideTools (module) pyrosetta.rosetta.core.chemical.orbitals (module) pyrosetta.rosetta.core.chemical.rings (module) pyrosetta.rosetta.core.chemical.rna (module) pyrosetta.rosetta.core.chemical.rotamers (module) pyrosetta.rosetta.core.chemical.sdf (module) pyrosetta.rosetta.core.conformation (module) pyrosetta.rosetta.core.conformation.carbohydrates (module) pyrosetta.rosetta.core.conformation.membrane (module) pyrosetta.rosetta.core.conformation.orbitals (module) pyrosetta.rosetta.core.conformation.parametric (module) pyrosetta.rosetta.core.conformation.residue_datacache (module) pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType (module) pyrosetta.rosetta.core.conformation.signals (module) pyrosetta.rosetta.core.conformation.symmetry (module) pyrosetta.rosetta.core.environment (module) pyrosetta.rosetta.core.enzymes (module) pyrosetta.rosetta.core.fragment (module) pyrosetta.rosetta.core.fragment.picking_old (module) pyrosetta.rosetta.core.fragment.picking_old.concepts (module) pyrosetta.rosetta.core.fragment.picking_old.vall (module) pyrosetta.rosetta.core.fragment.picking_old.vall.eval (module) pyrosetta.rosetta.core.fragment.picking_old.vall.gen (module) pyrosetta.rosetta.core.fragment.picking_old.vall.scores (module) pyrosetta.rosetta.core.fragment.rna (module) pyrosetta.rosetta.core.grid (module) pyrosetta.rosetta.core.id (module) pyrosetta.rosetta.core.import_pose (module) pyrosetta.rosetta.core.import_pose.atom_tree_diffs (module) pyrosetta.rosetta.core.import_pose.libraries (module) pyrosetta.rosetta.core.import_pose.options (module) pyrosetta.rosetta.core.import_pose.pose_stream (module) pyrosetta.rosetta.core.indexed_structure_store (module) pyrosetta.rosetta.core.init (module) pyrosetta.rosetta.core.io (module) pyrosetta.rosetta.core.io.carbohydrates (module) pyrosetta.rosetta.core.io.external (module) pyrosetta.rosetta.core.io.mmcif (module) pyrosetta.rosetta.core.io.pdb (module) pyrosetta.rosetta.core.io.pose_from_sfr (module) pyrosetta.rosetta.core.io.pose_to_sfr (module) pyrosetta.rosetta.core.io.PositionDdGInfo (module) pyrosetta.rosetta.core.io.raw_data (module) pyrosetta.rosetta.core.io.rna (module) pyrosetta.rosetta.core.io.sequence_comparation (module) pyrosetta.rosetta.core.io.serialization (module) pyrosetta.rosetta.core.io.silent (module) pyrosetta.rosetta.core.kinematics (module) pyrosetta.rosetta.core.kinematics.tree (module) pyrosetta.rosetta.core.membrane (module) pyrosetta.rosetta.core.optimization (module) pyrosetta.rosetta.core.optimization.symmetry (module) pyrosetta.rosetta.core.pack (module) pyrosetta.rosetta.core.pack.annealer (module) pyrosetta.rosetta.core.pack.dunbrack (module) pyrosetta.rosetta.core.pack.dunbrack.cenrot (module) pyrosetta.rosetta.core.pack.guidance_scoreterms (module) pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty (module) pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph (module) pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy (module) pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy (module) pyrosetta.rosetta.core.pack.hbonds (module) pyrosetta.rosetta.core.pack.interaction_graph (module) pyrosetta.rosetta.core.pack.rotamer_set (module) pyrosetta.rosetta.core.pack.rotamer_set.symmetry (module) pyrosetta.rosetta.core.pack.rotamers (module) pyrosetta.rosetta.core.pack.scmin (module) pyrosetta.rosetta.core.pack.task (module) pyrosetta.rosetta.core.pack.task.operation (module) pyrosetta.rosetta.core.pack.task.residue_selector (module) pyrosetta.rosetta.core.pack.task.rna (module) pyrosetta.rosetta.core.pose (module) pyrosetta.rosetta.core.pose.carbohydrates (module) pyrosetta.rosetta.core.pose.copydofs (module) pyrosetta.rosetta.core.pose.datacache (module) pyrosetta.rosetta.core.pose.full_model_info (module) pyrosetta.rosetta.core.pose.metrics (module) pyrosetta.rosetta.core.pose.metrics.simple_calculators (module) pyrosetta.rosetta.core.pose.motif (module) pyrosetta.rosetta.core.pose.ncbb (module) pyrosetta.rosetta.core.pose.reference_pose (module) pyrosetta.rosetta.core.pose.rna (module) pyrosetta.rosetta.core.pose.rna.secstruct_legacy (module) pyrosetta.rosetta.core.pose.signals (module) pyrosetta.rosetta.core.pose.symmetry (module) pyrosetta.rosetta.core.pose.toolbox (module) pyrosetta.rosetta.core.scoring (module) pyrosetta.rosetta.core.scoring.aa_composition_energy (module) pyrosetta.rosetta.core.scoring.aa_repeat_energy (module) pyrosetta.rosetta.core.scoring.annealing (module) pyrosetta.rosetta.core.scoring.bin_transitions (module) pyrosetta.rosetta.core.scoring.carbohydrates (module) pyrosetta.rosetta.core.scoring.carbon_hbonds (module) pyrosetta.rosetta.core.scoring.constraints (module) pyrosetta.rosetta.core.scoring.cryst (module) pyrosetta.rosetta.core.scoring.custom_pair_distance (module) pyrosetta.rosetta.core.scoring.disulfides (module) pyrosetta.rosetta.core.scoring.dna (module) pyrosetta.rosetta.core.scoring.dssp (module) pyrosetta.rosetta.core.scoring.elec (module) pyrosetta.rosetta.core.scoring.elec.electrie (module) pyrosetta.rosetta.core.scoring.electron_density (module) pyrosetta.rosetta.core.scoring.electron_density_atomwise (module) pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType (module) pyrosetta.rosetta.core.scoring.etable (module) pyrosetta.rosetta.core.scoring.etable.coulomb (module) pyrosetta.rosetta.core.scoring.etable.count_pair (module) pyrosetta.rosetta.core.scoring.etable.etrie (module) pyrosetta.rosetta.core.scoring.fiber_diffraction (module) pyrosetta.rosetta.core.scoring.func (module) pyrosetta.rosetta.core.scoring.geometric_solvation (module) pyrosetta.rosetta.core.scoring.hackaro (module) pyrosetta.rosetta.core.scoring.hbonds (module) pyrosetta.rosetta.core.scoring.hbonds.graph (module) pyrosetta.rosetta.core.scoring.hbonds.hbtrie (module) pyrosetta.rosetta.core.scoring.interface_ (module) pyrosetta.rosetta.core.scoring.lkball (module) pyrosetta.rosetta.core.scoring.lkball.lkbtrie (module) pyrosetta.rosetta.core.scoring.loop_graph (module) pyrosetta.rosetta.core.scoring.loop_graph.evaluator (module) pyrosetta.rosetta.core.scoring.magnesium (module) pyrosetta.rosetta.core.scoring.membrane (module) pyrosetta.rosetta.core.scoring.methods (module) pyrosetta.rosetta.core.scoring.methods.carbohydrates (module) pyrosetta.rosetta.core.scoring.methods.dfire (module) pyrosetta.rosetta.core.scoring.mm (module) pyrosetta.rosetta.core.scoring.mm.mmtrie (module) pyrosetta.rosetta.core.scoring.motif (module) pyrosetta.rosetta.core.scoring.netcharge_energy (module) pyrosetta.rosetta.core.scoring.nv (module) pyrosetta.rosetta.core.scoring.orbitals (module) pyrosetta.rosetta.core.scoring.packing (module) pyrosetta.rosetta.core.scoring.packstat (module) pyrosetta.rosetta.core.scoring.packstat.old (module) pyrosetta.rosetta.core.scoring.power_diagram (module) pyrosetta.rosetta.core.scoring.rna (module) pyrosetta.rosetta.core.scoring.rna.chemical_shift (module) pyrosetta.rosetta.core.scoring.rna.data (module) pyrosetta.rosetta.core.scoring.sasa (module) pyrosetta.rosetta.core.scoring.saxs (module) pyrosetta.rosetta.core.scoring.sc (module) pyrosetta.rosetta.core.scoring.solid_surface (module) pyrosetta.rosetta.core.scoring.sym_e (module) pyrosetta.rosetta.core.scoring.symmetry (module) pyrosetta.rosetta.core.scoring.trie (module) pyrosetta.rosetta.core.scoring.util_methods (module) pyrosetta.rosetta.core.scoring.vdwaals (module) pyrosetta.rosetta.core.select (module) pyrosetta.rosetta.core.select.jump_selector (module) pyrosetta.rosetta.core.select.movemap (module) pyrosetta.rosetta.core.select.residue_selector (module) pyrosetta.rosetta.core.select.util (module) pyrosetta.rosetta.core.sequence (module) pyrosetta.rosetta.core.simple_metrics (module) pyrosetta.rosetta.core.simple_metrics.metrics (module) pyrosetta.rosetta.core.util (module) pyrosetta.rosetta.cppdb (module) pyrosetta.rosetta.numeric (module) pyrosetta.rosetta.numeric.conversions (module) pyrosetta.rosetta.numeric.crick_equations (module) pyrosetta.rosetta.numeric.expression_parser (module) pyrosetta.rosetta.numeric.fourier (module) pyrosetta.rosetta.numeric.geometry (module) pyrosetta.rosetta.numeric.geometry.hashing (module) pyrosetta.rosetta.numeric.histograms (module) pyrosetta.rosetta.numeric.interpolation (module) pyrosetta.rosetta.numeric.interpolation.spline (module) pyrosetta.rosetta.numeric.kdtree (module) pyrosetta.rosetta.numeric.kinematic_closure (module) pyrosetta.rosetta.numeric.kinematic_closure.radians (module) pyrosetta.rosetta.numeric.linear_algebra (module) pyrosetta.rosetta.numeric.model_quality (module) pyrosetta.rosetta.numeric.nls (module) pyrosetta.rosetta.numeric.random (module) pyrosetta.rosetta.numeric.statistics (module) pyrosetta.rosetta.ObjexxFCL (module) pyrosetta.rosetta.ObjexxFCL.bit (module) pyrosetta.rosetta.ObjexxFCL.format (module) pyrosetta.rosetta.ObjexxFCL.Fortran (module) pyrosetta.rosetta.ObjexxFCL.internal (module) pyrosetta.rosetta.ObjexxFCL.internal.ObserverMediator (module) pyrosetta.rosetta.protocols (module) pyrosetta.rosetta.protocols.aa_composition (module) pyrosetta.rosetta.protocols.abinitio (module) pyrosetta.rosetta.protocols.abinitio.abscript (module) pyrosetta.rosetta.protocols.analysis (module) pyrosetta.rosetta.protocols.analysis.burial_metrics (module) pyrosetta.rosetta.protocols.analysis.simple_metrics (module) pyrosetta.rosetta.protocols.anchored_design (module) pyrosetta.rosetta.protocols.antibody (module) pyrosetta.rosetta.protocols.antibody.clusters (module) pyrosetta.rosetta.protocols.antibody.constraints (module) pyrosetta.rosetta.protocols.antibody.design (module) pyrosetta.rosetta.protocols.antibody.grafting (module) pyrosetta.rosetta.protocols.antibody.residue_selector (module) pyrosetta.rosetta.protocols.antibody.snugdock (module) pyrosetta.rosetta.protocols.antibody.task_operations (module) pyrosetta.rosetta.protocols.antibody_legacy (module) pyrosetta.rosetta.protocols.backbone_moves (module) pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover (module) pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers (module) pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers (module) pyrosetta.rosetta.protocols.backrub (module) pyrosetta.rosetta.protocols.branch_angle (module) pyrosetta.rosetta.protocols.calc_taskop_filters (module) pyrosetta.rosetta.protocols.calc_taskop_movers (module) pyrosetta.rosetta.protocols.canonical_sampling (module) pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks (module) pyrosetta.rosetta.protocols.carbohydrates (module) pyrosetta.rosetta.protocols.cartesian (module) pyrosetta.rosetta.protocols.checkpoint (module) pyrosetta.rosetta.protocols.cluster (module) pyrosetta.rosetta.protocols.cluster.calibur (module) pyrosetta.rosetta.protocols.comparative_modeling (module) pyrosetta.rosetta.protocols.comparative_modeling.features (module) pyrosetta.rosetta.protocols.constraint_filters (module) pyrosetta.rosetta.protocols.constraint_generator (module) pyrosetta.rosetta.protocols.constraint_movers (module) pyrosetta.rosetta.protocols.constraints_additional (module) pyrosetta.rosetta.protocols.contact_map (module) pyrosetta.rosetta.protocols.coupled_moves (module) pyrosetta.rosetta.protocols.cryst (module) pyrosetta.rosetta.protocols.cyclic_peptide (module) pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker (module) pyrosetta.rosetta.protocols.cyclic_peptide_predict (module) pyrosetta.rosetta.protocols.ddG (module) pyrosetta.rosetta.protocols.ddg (module) pyrosetta.rosetta.protocols.denovo_design (module) pyrosetta.rosetta.protocols.denovo_design.architects (module) pyrosetta.rosetta.protocols.denovo_design.components (module) pyrosetta.rosetta.protocols.denovo_design.connection (module) pyrosetta.rosetta.protocols.denovo_design.constraints (module) pyrosetta.rosetta.protocols.denovo_design.filters (module) pyrosetta.rosetta.protocols.denovo_design.movers (module) pyrosetta.rosetta.protocols.denovo_design.residue_selectors (module) pyrosetta.rosetta.protocols.denovo_design.task_operations (module) pyrosetta.rosetta.protocols.design_opt (module) pyrosetta.rosetta.protocols.dna (module) pyrosetta.rosetta.protocols.dna_dock (module) pyrosetta.rosetta.protocols.docking (module) pyrosetta.rosetta.protocols.docking.membrane (module) pyrosetta.rosetta.protocols.docking.stateless (module) pyrosetta.rosetta.protocols.domain_assembly (module) pyrosetta.rosetta.protocols.electron_density (module) pyrosetta.rosetta.protocols.energy_based_clustering (module) pyrosetta.rosetta.protocols.environment (module) pyrosetta.rosetta.protocols.environment.claims (module) pyrosetta.rosetta.protocols.enzdes (module) pyrosetta.rosetta.protocols.enzdes.enzutil (module) pyrosetta.rosetta.protocols.enzymatic_movers (module) pyrosetta.rosetta.protocols.evaluation (module) pyrosetta.rosetta.protocols.evolution (module) pyrosetta.rosetta.protocols.evolution.AlignmentCleanerTools (module) pyrosetta.rosetta.protocols.farnesyl (module) pyrosetta.rosetta.protocols.features (module) pyrosetta.rosetta.protocols.features.helixAssembly (module) pyrosetta.rosetta.protocols.features.RelevantResiduesMode (module) pyrosetta.rosetta.protocols.features.strand_assembly (module) pyrosetta.rosetta.protocols.fibril (module) pyrosetta.rosetta.protocols.filters (module) pyrosetta.rosetta.protocols.fldsgn (module) pyrosetta.rosetta.protocols.fldsgn.filters (module) pyrosetta.rosetta.protocols.fldsgn.potentials (module) pyrosetta.rosetta.protocols.fldsgn.potentials.sspot (module) pyrosetta.rosetta.protocols.fldsgn.topology (module) pyrosetta.rosetta.protocols.flexpack (module) pyrosetta.rosetta.protocols.flexpack.annealer (module) pyrosetta.rosetta.protocols.flexpack.interaction_graph (module) pyrosetta.rosetta.protocols.flexpack.rotamer_set (module) pyrosetta.rosetta.protocols.flexpep_docking (module) pyrosetta.rosetta.protocols.floppy_tail (module) pyrosetta.rosetta.protocols.flxbb (module) pyrosetta.rosetta.protocols.fold_from_loops (module) pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator (module) pyrosetta.rosetta.protocols.fold_from_loops.filters (module) pyrosetta.rosetta.protocols.fold_from_loops.movers (module) pyrosetta.rosetta.protocols.fold_from_loops.selectors (module) pyrosetta.rosetta.protocols.fold_from_loops.utils (module) pyrosetta.rosetta.protocols.forge (module) pyrosetta.rosetta.protocols.forge.build (module) pyrosetta.rosetta.protocols.forge.build.BuildInstructionState (module) pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme (module) pyrosetta.rosetta.protocols.forge.components (module) pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage (module) pyrosetta.rosetta.protocols.forge.constraints (module) pyrosetta.rosetta.protocols.forge.methods (module) pyrosetta.rosetta.protocols.forge.remodel (module) pyrosetta.rosetta.protocols.frag_picker (module) pyrosetta.rosetta.protocols.frag_picker.nonlocal (module) pyrosetta.rosetta.protocols.frag_picker.quota (module) pyrosetta.rosetta.protocols.frag_picker.scores (module) pyrosetta.rosetta.protocols.frags (module) pyrosetta.rosetta.protocols.generalized_kinematic_closure (module) pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter (module) pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber (module) pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector (module) pyrosetta.rosetta.protocols.genetic_algorithm (module) pyrosetta.rosetta.protocols.geometry (module) pyrosetta.rosetta.protocols.grafting (module) pyrosetta.rosetta.protocols.grafting.simple_movers (module) pyrosetta.rosetta.protocols.hbnet (module) pyrosetta.rosetta.protocols.helical_bundle (module) pyrosetta.rosetta.protocols.helical_bundle.parameters (module) pyrosetta.rosetta.protocols.helix_capper (module) pyrosetta.rosetta.protocols.hotspot_hashing (module) pyrosetta.rosetta.protocols.hotspot_hashing.movers (module) pyrosetta.rosetta.protocols.hybridization (module) pyrosetta.rosetta.protocols.hydrate (module) pyrosetta.rosetta.protocols.idealize (module) pyrosetta.rosetta.protocols.indel (module) pyrosetta.rosetta.protocols.indexed_structure_store (module) pyrosetta.rosetta.protocols.indexed_structure_store.filters (module) pyrosetta.rosetta.protocols.init (module) pyrosetta.rosetta.protocols.interface (module) pyrosetta.rosetta.protocols.jd2 (module) pyrosetta.rosetta.protocols.jd2.archive (module) pyrosetta.rosetta.protocols.jd2.JobInputterInputSource (module) pyrosetta.rosetta.protocols.jd3 (module) pyrosetta.rosetta.protocols.jd3.dag_node_managers (module) pyrosetta.rosetta.protocols.jd3.deallocation (module) pyrosetta.rosetta.protocols.jd3.output (module) pyrosetta.rosetta.protocols.jd3.pose_inputters (module) pyrosetta.rosetta.protocols.jd3.pose_outputters (module) pyrosetta.rosetta.protocols.jd3.standard (module) pyrosetta.rosetta.protocols.jobdist (module) pyrosetta.rosetta.protocols.jumping (module) pyrosetta.rosetta.protocols.kinematic_closure (module) pyrosetta.rosetta.protocols.kinematic_closure.perturbers (module) pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers (module) pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers (module) pyrosetta.rosetta.protocols.kinmatch (module) pyrosetta.rosetta.protocols.legacy_sewing (module) pyrosetta.rosetta.protocols.legacy_sewing.sampling (module) pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements (module) pyrosetta.rosetta.protocols.legacy_sewing.scoring (module) pyrosetta.rosetta.protocols.ligand_docking (module) pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock (module) pyrosetta.rosetta.protocols.ligand_docking.ligand_options (module) pyrosetta.rosetta.protocols.ligand_docking.rdf (module) pyrosetta.rosetta.protocols.loop_build (module) pyrosetta.rosetta.protocols.loop_grower (module) pyrosetta.rosetta.protocols.loop_modeler (module) pyrosetta.rosetta.protocols.loop_modeler.perturbers (module) pyrosetta.rosetta.protocols.loop_modeling (module) pyrosetta.rosetta.protocols.loop_modeling.refiners (module) pyrosetta.rosetta.protocols.loop_modeling.samplers (module) pyrosetta.rosetta.protocols.loop_modeling.utilities (module) pyrosetta.rosetta.protocols.loophash (module) pyrosetta.rosetta.protocols.loops (module) pyrosetta.rosetta.protocols.loops.filters (module) pyrosetta.rosetta.protocols.loops.loop_closure (module) pyrosetta.rosetta.protocols.loops.loop_closure.ccd (module) pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure (module) pyrosetta.rosetta.protocols.loops.loop_mover (module) pyrosetta.rosetta.protocols.loops.loop_mover.perturb (module) pyrosetta.rosetta.protocols.loops.loop_mover.refine (module) pyrosetta.rosetta.protocols.loops.loops_definers (module) pyrosetta.rosetta.protocols.magnesium (module) pyrosetta.rosetta.protocols.make_rot_lib (module) pyrosetta.rosetta.protocols.match (module) pyrosetta.rosetta.protocols.match.downstream (module) pyrosetta.rosetta.protocols.match.output (module) pyrosetta.rosetta.protocols.match.upstream (module) pyrosetta.rosetta.protocols.matdes (module) pyrosetta.rosetta.protocols.md (module) pyrosetta.rosetta.protocols.mean_field (module) pyrosetta.rosetta.protocols.medal (module) pyrosetta.rosetta.protocols.membrane (module) pyrosetta.rosetta.protocols.membrane.benchmark (module) pyrosetta.rosetta.protocols.membrane.geometry (module) pyrosetta.rosetta.protocols.membrane.symmetry (module) pyrosetta.rosetta.protocols.membrane.visualize (module) pyrosetta.rosetta.protocols.metal_interface (module) pyrosetta.rosetta.protocols.minimization_packing (module) pyrosetta.rosetta.protocols.minimization_packing.symmetry (module) pyrosetta.rosetta.protocols.monte_carlo (module) pyrosetta.rosetta.protocols.motif_grafting (module) pyrosetta.rosetta.protocols.motif_grafting.movers (module) pyrosetta.rosetta.protocols.motifs (module) pyrosetta.rosetta.protocols.moves (module) pyrosetta.rosetta.protocols.mpi_refinement (module) pyrosetta.rosetta.protocols.multistage_rosetta_scripts (module) pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster (module) pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics (module) pyrosetta.rosetta.protocols.multistate_design (module) pyrosetta.rosetta.protocols.ncbb (module) pyrosetta.rosetta.protocols.ncbb.oop (module) pyrosetta.rosetta.protocols.neighbor (module) pyrosetta.rosetta.protocols.noesy_assign (module) pyrosetta.rosetta.protocols.nonlocal (module) pyrosetta.rosetta.protocols.normalmode (module) pyrosetta.rosetta.protocols.optimize_weights (module) pyrosetta.rosetta.protocols.pack_daemon (module) pyrosetta.rosetta.protocols.parser (module) pyrosetta.rosetta.protocols.pb_potential (module) pyrosetta.rosetta.protocols.peptide_deriver (module) pyrosetta.rosetta.protocols.pmut_scan (module) pyrosetta.rosetta.protocols.pockets (module) pyrosetta.rosetta.protocols.pose_creation (module) pyrosetta.rosetta.protocols.pose_length_moves (module) pyrosetta.rosetta.protocols.pose_metric_calculators (module) pyrosetta.rosetta.protocols.pose_reporters (module) pyrosetta.rosetta.protocols.pose_selectors (module) pyrosetta.rosetta.protocols.protein_interface_design (module) pyrosetta.rosetta.protocols.protein_interface_design.filters (module) pyrosetta.rosetta.protocols.protein_interface_design.movers (module) pyrosetta.rosetta.protocols.qsar (module) pyrosetta.rosetta.protocols.qsar.scoring_grid (module) pyrosetta.rosetta.protocols.rbsegment_relax (module) pyrosetta.rosetta.protocols.recces (module) pyrosetta.rosetta.protocols.recces.options (module) pyrosetta.rosetta.protocols.recces.params (module) pyrosetta.rosetta.protocols.recces.sampler (module) pyrosetta.rosetta.protocols.recces.sampler.rna (module) pyrosetta.rosetta.protocols.recces.scratch (module) pyrosetta.rosetta.protocols.relax (module) pyrosetta.rosetta.protocols.relax.membrane (module) pyrosetta.rosetta.protocols.residue_optimization (module) pyrosetta.rosetta.protocols.residue_selectors (module) pyrosetta.rosetta.protocols.rigid (module) pyrosetta.rosetta.protocols.rna (module) pyrosetta.rosetta.protocols.rna.denovo (module) pyrosetta.rosetta.protocols.rna.denovo.coarse (module) pyrosetta.rosetta.protocols.rna.denovo.movers (module) pyrosetta.rosetta.protocols.rna.denovo.output (module) pyrosetta.rosetta.protocols.rna.movers (module) pyrosetta.rosetta.protocols.rna.setup (module) pyrosetta.rosetta.protocols.rosetta_scripts (module) pyrosetta.rosetta.protocols.rotamer_recovery (module) pyrosetta.rosetta.protocols.RotamerDump (module) pyrosetta.rosetta.protocols.rpc (module) pyrosetta.rosetta.protocols.sasa_scores (module) pyrosetta.rosetta.protocols.score_filters (module) pyrosetta.rosetta.protocols.scoring (module) pyrosetta.rosetta.protocols.scoring.methods (module) pyrosetta.rosetta.protocols.scoring.methods.pcs (module) pyrosetta.rosetta.protocols.scoring.methods.pcs2 (module) pyrosetta.rosetta.protocols.scoring.methods.pcsTs1 (module) pyrosetta.rosetta.protocols.scoring.methods.pcsTs2 (module) pyrosetta.rosetta.protocols.scoring.methods.pcsTs3 (module) pyrosetta.rosetta.protocols.scoring.methods.pcsTs4 (module) pyrosetta.rosetta.protocols.scoring.methods.saxs (module) pyrosetta.rosetta.protocols.seeded_abinitio (module) pyrosetta.rosetta.protocols.sic_dock (module) pyrosetta.rosetta.protocols.sic_dock.scores (module) pyrosetta.rosetta.protocols.simple_ddg (module) pyrosetta.rosetta.protocols.simple_filters (module) pyrosetta.rosetta.protocols.simple_moves (module) pyrosetta.rosetta.protocols.simple_moves.a3b_hbs (module) pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock (module) pyrosetta.rosetta.protocols.simple_moves.bb_sampler (module) pyrosetta.rosetta.protocols.simple_moves.bin_transitions (module) pyrosetta.rosetta.protocols.simple_moves.chiral (module) pyrosetta.rosetta.protocols.simple_moves.hbs (module) pyrosetta.rosetta.protocols.simple_moves.oop (module) pyrosetta.rosetta.protocols.simple_moves.rational_mc (module) pyrosetta.rosetta.protocols.simple_moves.sidechain_moves (module) pyrosetta.rosetta.protocols.simple_moves.triazolamer (module) pyrosetta.rosetta.protocols.simple_pose_metric_calculators (module) pyrosetta.rosetta.protocols.simple_task_operations (module) pyrosetta.rosetta.protocols.sparta (module) pyrosetta.rosetta.protocols.ss_prediction (module) pyrosetta.rosetta.protocols.star (module) pyrosetta.rosetta.protocols.stepwise (module) pyrosetta.rosetta.protocols.stepwise.legacy (module) pyrosetta.rosetta.protocols.stepwise.legacy.modeler (module) pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein (module) pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna (module) pyrosetta.rosetta.protocols.stepwise.legacy.screener (module) pyrosetta.rosetta.protocols.stepwise.modeler (module) pyrosetta.rosetta.protocols.stepwise.modeler.align (module) pyrosetta.rosetta.protocols.stepwise.modeler.movemap (module) pyrosetta.rosetta.protocols.stepwise.modeler.options (module) pyrosetta.rosetta.protocols.stepwise.modeler.packer (module) pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens (module) pyrosetta.rosetta.protocols.stepwise.modeler.precomputed (module) pyrosetta.rosetta.protocols.stepwise.modeler.protein (module) pyrosetta.rosetta.protocols.stepwise.modeler.protein.checker (module) pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close (module) pyrosetta.rosetta.protocols.stepwise.modeler.rna (module) pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge (module) pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker (module) pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime (module) pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate (module) pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body (module) pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar (module) pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters (module) pyrosetta.rosetta.protocols.stepwise.monte_carlo (module) pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover (module) pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options (module) pyrosetta.rosetta.protocols.stepwise.monte_carlo.options (module) pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna (module) pyrosetta.rosetta.protocols.stepwise.monte_carlo.submotif (module) pyrosetta.rosetta.protocols.stepwise.options (module) pyrosetta.rosetta.protocols.stepwise.sampler (module) pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs (module) pyrosetta.rosetta.protocols.stepwise.sampler.input_streams (module) pyrosetta.rosetta.protocols.stepwise.sampler.jump (module) pyrosetta.rosetta.protocols.stepwise.sampler.protein (module) pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body (module) pyrosetta.rosetta.protocols.stepwise.sampler.rna (module) pyrosetta.rosetta.protocols.stepwise.sampler.screener (module) pyrosetta.rosetta.protocols.stepwise.screener (module) pyrosetta.rosetta.protocols.stepwise.setup (module) pyrosetta.rosetta.protocols.struct_fragment (module) pyrosetta.rosetta.protocols.surface_docking (module) pyrosetta.rosetta.protocols.symmetric_docking (module) pyrosetta.rosetta.protocols.symmetric_docking.membrane (module) pyrosetta.rosetta.protocols.symmetry (module) pyrosetta.rosetta.protocols.task_operations (module) pyrosetta.rosetta.protocols.toolbox (module) pyrosetta.rosetta.protocols.toolbox.match_enzdes_util (module) pyrosetta.rosetta.protocols.toolbox.pose_manipulation (module) pyrosetta.rosetta.protocols.toolbox.rigid_body (module) pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations (module) pyrosetta.rosetta.protocols.toolbox.sample_around (module) pyrosetta.rosetta.protocols.topology_broker (module) pyrosetta.rosetta.protocols.topology_broker.claims (module) pyrosetta.rosetta.protocols.topology_broker.weights (module) pyrosetta.rosetta.protocols.trajectory (module) pyrosetta.rosetta.protocols.ub_e2c (module) pyrosetta.rosetta.protocols.unfolded_state_energy_calculator (module) pyrosetta.rosetta.protocols.vardist_solaccess (module) pyrosetta.rosetta.protocols.viewer (module) pyrosetta.rosetta.protocols.viewer.graphics_states_param (module) pyrosetta.rosetta.protocols.vip (module) pyrosetta.rosetta.protocols.wum (module) pyrosetta.rosetta.std (module) pyrosetta.rosetta.std.chrono (module) pyrosetta.rosetta.utility (module) pyrosetta.rosetta.utility.CSI (module) pyrosetta.rosetta.utility.excn (module) pyrosetta.rosetta.utility.factory (module) pyrosetta.rosetta.utility.file (module) pyrosetta.rosetta.utility.graph (module) pyrosetta.rosetta.utility.io (module) pyrosetta.rosetta.utility.io.mpi_stream (module) pyrosetta.rosetta.utility.json_spirit (module) pyrosetta.rosetta.utility.keys (module) pyrosetta.rosetta.utility.libsvm (module) pyrosetta.rosetta.utility.options (module) pyrosetta.rosetta.utility.py (module) pyrosetta.rosetta.utility.signals (module) pyrosetta.rosetta.utility.sql_database (module) pyrosetta.rosetta.utility.tag (module) pyrosetta.rosetta.utility.tools (module) pyrosetta.rosetta.utility.type_traits (module) pyrosetta.rosetta.utility.type_traits.has_insertion_operator_implementation (module) pyrosetta.rosetta.utility.xsd_util (module) pyrosetta.teaching (module) pyrosetta.toolbox (module) pyrosetta.toolbox.cleaning (module) pyrosetta.toolbox.extract_coords_pose (module) pyrosetta.toolbox.generate_resfile (module) pyrosetta.toolbox.mutants (module) pyrosetta.toolbox.numpy_utils (module) pyrosetta.toolbox.rcsb (module) pyrosetta.util (module) PythonLoggingSink (class in pyrosetta.logging_support) PyTracer (class in pyrosetta.rosetta.basic)

Q

q() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) Q() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) quadratic_chainbreak() (in module pyrosetta.rosetta.protocols.forge.methods) quadratic_deriv_interpolation() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) quadratic_interpolation() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) quadrupole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) quat2R() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.protocols.simple_filters) QuenchDirection (class in pyrosetta.rosetta.protocols.carbohydrates) query_length() (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method)

query_name() (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation method) query_selector() (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) quick_ring_detection() (in module pyrosetta.rosetta.core.chemical) QuickRelaxPartnersSeparatelyCreator (class in pyrosetta.rosetta.protocols.docking.membrane) QuickRepacker (class in pyrosetta.rosetta.protocols.pack_daemon) quota_protocol() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) quota_score() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) QuotaCollector (class in pyrosetta.rosetta.protocols.frag_picker.quota) QuotaConfig (class in pyrosetta.rosetta.protocols.frag_picker.quota) QuotaPool (class in pyrosetta.rosetta.protocols.frag_picker.quota) QuotaSelector (class in pyrosetta.rosetta.protocols.frag_picker.quota) quoted_split() (in module pyrosetta.rosetta.utility)

R

R() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) r0() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) r1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) r1_vect() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) R2quat() (in module pyrosetta.rosetta.protocols.simple_filters) rad() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) rad2() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) radial_bin_index() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) radial_count() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) radial_disp() (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) radial_lookup() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) radial_lookup_withkey() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) radians() (in module pyrosetta.rosetta.numeric.conversions) radius_for_attype() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) RadiusOfGyrationFeaturesCreator (class in pyrosetta.rosetta.protocols.features) rama() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) Rama2bPerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) rama_cutoff_energy() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) rama_delta() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) rama_prepro_multiplier() (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) Rama_Table_Type (class in pyrosetta.rosetta.core.scoring) RamachandranHash (class in pyrosetta.rosetta.protocols.features) RamaMutationSelector (class in pyrosetta.rosetta.protocols.cyclic_peptide) RamaPerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) RamaPreproFilename (class in pyrosetta.rosetta.core.chemical) RamaPreproResname (class in pyrosetta.rosetta.core.chemical) RamaScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) ramp_down_constraints() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) ramp_minpack_loop() (in module pyrosetta.rosetta.protocols.mpi_refinement) ramp_minpack_pose() (in module pyrosetta.rosetta.protocols.mpi_refinement) rand_sleep() (in module pyrosetta.rosetta.utility) random() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) random_angle() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) random_chunk_insertion() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) random_connection() (in module pyrosetta.rosetta.protocols.ligand_docking) random_delay() (in module pyrosetta.rosetta.core.init) random_entity() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) random_fragment_insertion() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) random_mode() (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) random_mover() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) random_normal() (in module pyrosetta.rosetta.numeric.random) random_perturbation() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) random_range() (in module pyrosetta.rosetta.numeric.random) (pyrosetta.rosetta.numeric.random.RandomGenerator method) random_range2() (pyrosetta.rosetta.numeric.random.RandomGenerator method) random_reorientation_matrix() (in module pyrosetta.rosetta.protocols.geometry) random_rotation() (in module pyrosetta.rosetta.core.scoring.motif) (in module pyrosetta.rosetta.numeric.random) random_torsion_move() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) random_trans() (pyrosetta.rosetta.core.kinematics.Jump method) random_tree_from_jump_points() (pyrosetta.rosetta.core.kinematics.FoldTree method) random_unit_quaternion() (in module pyrosetta.rosetta.numeric.random) random_vector() (in module pyrosetta.rosetta.numeric.random) random_vector_spherical() (in module pyrosetta.rosetta.numeric.random) random_vector_unit_cube() (in module pyrosetta.rosetta.numeric.random) random_xform() (in module pyrosetta.rosetta.numeric.random) randomAngle() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) RandomConformerMover (class in pyrosetta.rosetta.protocols.ligand_docking) RandomGapSolutionPicker (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers) RandomGenerator (class in pyrosetta.rosetta.numeric.random) RandomGlycanFoliageSelector (class in pyrosetta.rosetta.core.select.residue_selector) randomize() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) randomize_glycan_torsions() (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) randomize_loop() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) randomize_loops() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) randomize_missing_coords() (in module pyrosetta.rosetta.core.io.pose_from_sfr) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) randomize_pose_rigid_bodies() (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) randomize_selected_atoms() (in module pyrosetta.rosetta.protocols.comparative_modeling) randomize_stage() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) RandomMover (class in pyrosetta.rosetta.protocols.moves) RandomMutation (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) RandomOmegaFlipMover (class in pyrosetta.rosetta.protocols.simple_moves) RandomPositionRotationMover (class in pyrosetta.rosetta.protocols.membrane) RandomPositionTranslationMover (class in pyrosetta.rosetta.protocols.membrane) RandomResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) RandomSheetBuilder (class in pyrosetta.rosetta.protocols.jumping) RandomSolutions (class in pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers) RandomTorsionMover (class in pyrosetta.rosetta.protocols.simple_moves) RandomTorsionPoseFolder (class in pyrosetta.rosetta.protocols.denovo_design.components) range() (in module pyrosetta.rosetta.protocols.sic_dock) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) range_check() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) rank_score() (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) ranking_cenfilter() (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) ranking_fafilter() (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) RationalLoopComparator (class in pyrosetta.rosetta.protocols.loops) RationalMonteCarlo (class in pyrosetta.rosetta.protocols.simple_moves.rational_mc) raw_child_index() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_default_string() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) raw_get_nonjump_atom() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_input_stub_atom0() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_input_stub_atom1() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_input_stub_atom2() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_input_stub_atom3() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_parent() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_previous_child() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_previous_sibling() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_select() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) raw_stub_atom1() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_stub_atom2() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_stub_atom3() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_unfolded_state_energymap() (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential method) raw_value_string() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) RawFileData (class in pyrosetta.rosetta.core.io.raw_data) RawStruct (class in pyrosetta.rosetta.core.io.raw_data) rb_grid_rotamer_trials_atr_rep() (in module pyrosetta.rosetta.protocols.ligand_docking) rb_grid_score_atr_rep() (in module pyrosetta.rosetta.protocols.ligand_docking) rb_jump() (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) RB_lt (class in pyrosetta.rosetta.protocols.rbsegment_relax) rb_minimizable() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) rb_minimize_all_confs() (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) RBResidueRange (class in pyrosetta.rosetta.protocols.rbsegment_relax) RBSegment (class in pyrosetta.rosetta.protocols.rbsegment_relax) RBSegmentMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) RBSegmentRelax_main() (in module pyrosetta.rosetta.protocols) RBSegmentType (class in pyrosetta.rosetta.protocols.rbsegment_relax) rdbuf() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) RDC (class in pyrosetta.rosetta.core.scoring) RDC.RDC_TYPE (class in pyrosetta.rosetta.core.scoring) RDC_Rohl (class in pyrosetta.rosetta.core.scoring) RdcEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) RDCScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) RdcSelectEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) RdcTargetEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) rdf_function_ct_namer() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) rdf_function_group_name() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) RDFBinaryHbondCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFBinaryHbondFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFBinaryHbondFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFBinaryOrbitalFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFBinaryOrbitalFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFBinaryOrbitalFunctionCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFChargeCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFChargeFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFChargeFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFElecCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFElecFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFElecFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFEtableCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFEtableFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFEtableFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFFunctionCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFFunctionFactory (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFHbondCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFHbondFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFHbondFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFOrbitalFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFOrbitalFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFOrbitalFunctionCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) reachable_buried_volume() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) read() (in module pyrosetta.rosetta.ObjexxFCL) (in module pyrosetta.rosetta.utility.json_spirit) (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) read_additional_pdb_data() (in module pyrosetta.rosetta.core.import_pose) read_alignment_file() (in module pyrosetta.rosetta.core.sequence) read_all_alignments() (in module pyrosetta.rosetta.core.sequence) read_all_poses() (in module pyrosetta.rosetta.core.import_pose) read_aln() (in module pyrosetta.rosetta.core.sequence) read_alternative_3_letter_codes_from_database_file() (in module pyrosetta.rosetta.core.io) read_anchorfile() (pyrosetta.rosetta.protocols.anchored_design.Anchor method) read_binary() (in module pyrosetta.rosetta.core.io.serialization) read_biounit() (in module pyrosetta.rosetta.protocols.sic_dock) read_bond_file() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) read_center_normal_from_cmd() (in module pyrosetta.rosetta.protocols.membrane) read_center_normal_from_tag() (in module pyrosetta.rosetta.protocols.membrane) read_checkpoint() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) read_codes_and_roots_from_database_file() (in module pyrosetta.rosetta.core.chemical.carbohydrates) read_comment_pdb() (in module pyrosetta.rosetta.core.pose) read_config_file() (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) read_conformers_from_database_file_for_ring_size() (in module pyrosetta.rosetta.core.chemical.rings) read_constraint() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) read_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) read_constraints_new() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) read_cp_tables_from_db() (in module pyrosetta.rosetta.core.scoring.elec) read_data() (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) read_db() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) read_ddg_predictions_file() (in module pyrosetta.rosetta.core.io.PositionDdGInfo) read_def() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) read_depth() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_disulf_pairing_list() (in module pyrosetta.rosetta.protocols.jumping) read_enzyme_data_from_file() (in module pyrosetta.rosetta.core.enzymes) read_fasta_file() (in module pyrosetta.rosetta.core.sequence) read_fasta_file_and_concatenate() (in module pyrosetta.rosetta.core.sequence) read_fasta_file_return_str() (in module pyrosetta.rosetta.core.sequence) read_fasta_file_section() (in module pyrosetta.rosetta.core.sequence) read_fasta_file_str() (in module pyrosetta.rosetta.core.sequence) read_file() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.ElementSet method) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) read_file_into_string() (in module pyrosetta.rosetta.protocols.cyclic_peptide_predict) read_files_for_base_residue_types() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) read_files_for_unpatchable_residue_types() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) read_fold_tree() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) read_fold_tree_from_file() (in module pyrosetta.rosetta.protocols.backrub) read_fragment_file() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) read_fragment_stream() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) read_from_binary_file() (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) read_from_disk() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) read_from_file() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) read_from_file_no_filters() (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) read_from_stream() (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) read_Gaussian_parameters_from_database_file() (in module pyrosetta.rosetta.core.scoring.carbohydrates) read_general_aln() (in module pyrosetta.rosetta.core.sequence) read_general_aln_file() (in module pyrosetta.rosetta.core.sequence) read_glycan_sequence_file() (in module pyrosetta.rosetta.core.chemical.carbohydrates) read_grishin_aln_file() (in module pyrosetta.rosetta.core.sequence) read_H3_cter_fragment() (in module pyrosetta.rosetta.protocols.antibody_legacy) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) read_hyfile() (in module pyrosetta.rosetta.protocols.hydrate) read_in_amoeba_parameters() (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) read_in_and_recursively_replace_includes() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) read_in_and_set_disulfides() (pyrosetta.rosetta.core.io.raw_data.DisulfideFile method) read_in_structures() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) read_in_vdw_tinker_parameters() (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) read_individual_constraint_new() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) read_info_file() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) read_legacydb() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) read_loop_file() (pyrosetta.rosetta.protocols.loops.LoopsFileIO method) read_loop_file_stream() (pyrosetta.rosetta.protocols.loops.LoopsFileIO method) read_loop_fragments() (in module pyrosetta.rosetta.protocols.loops) read_loops_file() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) read_loops_options() (pyrosetta.rosetta.protocols.loops.Loops method) read_mArray() (in module pyrosetta.rosetta.utility.json_spirit) read_meta_file() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) read_metric_value() (in module pyrosetta.rosetta.basic) read_minor_helix_params() (in module pyrosetta.rosetta.protocols.helical_bundle) read_mObject() (in module pyrosetta.rosetta.utility.json_spirit) read_model_file() (in module pyrosetta.rosetta.protocols.legacy_sewing) read_motifs_binary() (in module pyrosetta.rosetta.core.scoring.motif) read_mover_weight() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) read_nomenclature_table_from_database_file() (in module pyrosetta.rosetta.core.chemical.carbohydrates) read_only_ATOM_entries() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) read_options() (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) read_or_throw() (in module pyrosetta.rosetta.utility.json_spirit) read_pairing_list() (in module pyrosetta.rosetta.core.scoring.dssp) read_params() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) read_pdb_header() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) read_peptide_design_file() (in module pyrosetta.rosetta.protocols.cyclic_peptide_predict) read_pose() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) read_pose_from_file() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) read_pose_numbered_loops_file() (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader method) read_probabilities_or_die() (in module pyrosetta.rosetta.numeric) read_psipred_ss2() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_psipred_ss2_file() (in module pyrosetta.rosetta.core.pose) read_RBSegment_file() (in module pyrosetta.rosetta.protocols.rbsegment_relax) read_RDC_file() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) read_ring_sizes_and_morphemes_from_database_file() (in module pyrosetta.rosetta.core.chemical.carbohydrates) read_score_headers() (pyrosetta.rosetta.core.io.silent.SilentStruct method) read_sequence() (pyrosetta.rosetta.core.io.silent.SilentStruct method) read_short_names_to_iupac_format_string() (in module pyrosetta.rosetta.core.chemical.carbohydrates) read_spine_x() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_ss2() (in module pyrosetta.rosetta.protocols.mpi_refinement) read_ss_file() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_ss_files() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_std_frags_from_cmd() (in module pyrosetta.rosetta.core.fragment) read_stream() (pyrosetta.rosetta.core.io.silent.SilentFileData method) read_structures() (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) read_tag() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) read_tags_fast() (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) read_talos_ss() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_topol_file() (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) read_topology_file() (in module pyrosetta.rosetta.core.chemical) read_vall() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_xfres_binary() (in module pyrosetta.rosetta.core.scoring.motif) ReadResfileAndObeyLengthEvents (class in pyrosetta.rosetta.core.pack.task.operation) readsome() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) readValueOrDie() (in module pyrosetta.rosetta.core.scoring.func) ready() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) ready_for_nonideal_scoring() (pyrosetta.rosetta.core.scoring.ScoreFunction method) ready_to_align() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) real2afteroption() (in module pyrosetta.rosetta.basic.options) Real2string() (in module pyrosetta.rosetta.utility) real3afteroption() (in module pyrosetta.rosetta.basic.options) real_regex_pattern() (in module pyrosetta.rosetta.utility.tag) real_to_virtual() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.pose.Pose method) realafteroption() (in module pyrosetta.rosetta.basic.options) RealAngleToShort() (in module pyrosetta.rosetta.protocols.loophash) RealFilter (class in pyrosetta.rosetta.core.chemical) RealMetric (class in pyrosetta.rosetta.core.simple_metrics) RealOption (class in pyrosetta.rosetta.utility.options) RealOptionKey (class in pyrosetta.rosetta.utility.options) RealVectorOption (class in pyrosetta.rosetta.utility.options) RealVectorOptionKey (class in pyrosetta.rosetta.utility.options) reassign_atoms_for_intra_residue_stubs() (pyrosetta.rosetta.core.kinematics.FoldTree method) rebuild_disulfide() (in module pyrosetta.rosetta.core.util) rebuild_fa_disulfides() (in module pyrosetta.rosetta.core.util) rebuild_loops_until_closed() (in module pyrosetta.rosetta.protocols.comparative_modeling) rebuild_missing_atoms() (in module pyrosetta.rosetta.protocols.denovo_design) rebuild_pdb2pose() (pyrosetta.rosetta.core.pose.PDBInfo method) rebuild_polymer_bond_dependent_atoms() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) rebuild_polymer_bond_dependent_atoms_this_residue_only() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) rebuild_residue_connection_dependent_atoms() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) recalculate_rmsd_and_output_silent_file() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) recalculate_transforms() (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) recalculate_z_coordinate() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) recces_pose_setup() (in module pyrosetta.rosetta.protocols.recces) receive_char_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) receive_double_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) receive_doubles_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) receive_integer_from_anyone() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) receive_integer_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) receive_integers_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) receive_message() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) receive_observers_from() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) receive_size_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) receive_sizes_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) receive_string_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) recent_history_queue (class in pyrosetta.rosetta.utility) recenter() (in module pyrosetta.rosetta.core.conformation.symmetry) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) record() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) record_endpoint() (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) record_match() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) record_move() (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) record_new_pose() (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) record_new_score_function() (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) record_new_temperature() (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) RecordCollection (class in pyrosetta.rosetta.core.io.pdb) RecordType (class in pyrosetta.rosetta.core.io.pdb) recover_checkpoint() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) recover_conformer_sidechains() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) recover_low() (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) recover_original_on_failure() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) recover_sidechains() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) recovery_rate() (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) recreate_task() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) recursive() (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) redefine_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) RedefineChi (class in pyrosetta.rosetta.core.chemical) redo() (pyrosetta.rosetta.protocols.jumping.SameStrand method) Reduced_Jdipolar() (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) reducible() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) ref() (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) ref_pose_for() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) reference() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) reference_copy() (pyrosetta.rosetta.ObjexxFCL.Dimension method) reference_name() (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) reference_pdb_id() (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation method) reference_pose() (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) reference_pose_cop() (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) reference_pose_from_current() (pyrosetta.rosetta.core.pose.Pose method) reference_pose_name() (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) reference_pose_set() (pyrosetta.rosetta.core.pose.Pose method) reference_pose_set_cop() (pyrosetta.rosetta.core.pose.Pose method) reference_selector() (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) ReferencePose (class in pyrosetta.rosetta.core.pose.reference_pose) ReferencePoseSet (class in pyrosetta.rosetta.core.pose.reference_pose) refpose_enabled_residue_number_string() (in module pyrosetta.rosetta.utility.tag) refresh_bbstub_constraints() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) refresh_coordinate_constraints() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) refresh_energy_cache() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) refuse_unexpected_files() (pyrosetta.rosetta.utility.io.FileContentsMap method) regenerate_model() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) RegEx_based_CDR_Detector (class in pyrosetta.rosetta.protocols.antibody.grafting) regex_usable() (in module pyrosetta.rosetta.core.select.residue_selector) RegExManager (class in pyrosetta.rosetta.protocols.antibody.grafting) region() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) region1() (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) region2() (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) region_all() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) region_simple() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) RegionalConnections (class in pyrosetta.rosetta.protocols.simple_filters) register_clash() (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) register_common_options() (in module pyrosetta.rosetta.protocols.abinitio) register_factory_prototypes() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) register_ff() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) register_hbond() (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) register_options() (in module pyrosetta.rosetta.protocols.evaluation) (in module pyrosetta.rosetta.protocols.jd2) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringProtocol method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) register_options_broker() (in module pyrosetta.rosetta.protocols.abinitio) register_options_universal_main() (in module pyrosetta.rosetta.protocols.jobdist) register_score_maker() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) register_variable_expression() (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) register_work_unit() (pyrosetta.rosetta.protocols.wum.WorkUnitList method) reindex_residues() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) reindex_sections() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) reinitialize() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) reinitialize_active_energy_methods() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) reinitialize_CCD_torsions() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) reinitialize_for_each_job() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) reinitialize_for_new_input() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) reinitialize_mingraph_neighborhood_for_residue() (in module pyrosetta.rosetta.core.pack) reinitialize_minnode_for_residue() (pyrosetta.rosetta.core.scoring.ScoreFunction method) reject_change() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) reject_mutant() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) rel_per_res_sc_sasa() (in module pyrosetta.rosetta.core.scoring.sasa) relative() (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) relative_pose_filter() (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) relative_pose_names() (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) RelativeConnectRight (class in pyrosetta.rosetta.protocols.forge.build) RelativeSegmentFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) RelativeSequencePosition (class in pyrosetta.rosetta.protocols.forge.build) relax() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) relax_cdrs() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) relax_interface() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) Relax_main() (in module pyrosetta.rosetta.protocols.relax) relax_mover() (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) relax_optimized_CDR_grafts() (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) relax_pose() (in module pyrosetta.rosetta.protocols.relax) release_buffers() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) ReleaseConstraintFromResidueMover (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) remainder() (in module pyrosetta.rosetta.numeric) remap() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) remap_allowed_residues_to_template() (pyrosetta.rosetta.protocols.task_operations.LinkResidues method) remap_atom_vds() (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) remap_cis_omega_torsion_bins_to_trans() (in module pyrosetta.rosetta.core.conformation) remap_pdb_atom_names() (pyrosetta.rosetta.core.chemical.ResidueType method) remap_rb_segments() (in module pyrosetta.rosetta.protocols.rbsegment_relax) remap_resid() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) remap_residue() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) remap_residue_level_tasks() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) remap_residue_positions() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) remapped_clone() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) remarks() (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.pose.PDBInfo method) remember_unrecognized_res() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) remember_unrecognized_water() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) remodel_fold_tree_to_account_for_insertion() (in module pyrosetta.rosetta.core.kinematics) remodel_generic_taskfactory() (in module pyrosetta.rosetta.protocols.forge.methods) RemodelConstraintGenerator (class in pyrosetta.rosetta.protocols.forge.remodel) remodelData() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) RemodelLoopMover (class in pyrosetta.rosetta.protocols.forge.remodel) RemodelLoopMoverPoseFolder (class in pyrosetta.rosetta.protocols.denovo_design.components) remove() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) remove_all_anchors_and_ENF() (in module pyrosetta.rosetta.protocols.hydrate) remove_all_enzdes_constraints() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) remove_all_jump_atoms() (in module pyrosetta.rosetta.protocols.denovo_design)

remove_all_variant_types() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) remove_all_virtual_phosphates() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) remove_and_store_bracketed() (in module pyrosetta.rosetta.core.pose.rna) remove_atom_info_from_vec_stable() (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) remove_atom_info_stable() (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) remove_bad_inputs_from_job_list() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) remove_base_residue_type() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) remove_bracketed() (in module pyrosetta.rosetta.core.pose.rna) remove_carbohydrate_branch_point_variants() (in module pyrosetta.rosetta.core.pose.carbohydrates) remove_chain_break_jump_point() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) remove_chain_break_variants() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) remove_chainbreaks_according_to_jumps() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) remove_checkpoint_file() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) remove_connection_inconsistencies() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) remove_constraint() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) remove_constraints() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) remove_constraints_of_type() (in module pyrosetta.rosetta.core.scoring.constraints) remove_coordinate_constraints_from_pose() (in module pyrosetta.rosetta.protocols.protein_interface_design) remove_covalent_connection_from_pose() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo method) remove_covalent_connections_from_pose() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) remove_cut() (in module pyrosetta.rosetta.protocols.jumping) remove_cutpoint() (in module pyrosetta.rosetta.protocols.forge.methods) remove_cutpoint_closed() (in module pyrosetta.rosetta.core.import_pose) remove_cutpoint_variants() (in module pyrosetta.rosetta.core.util) (in module pyrosetta.rosetta.protocols.forge.methods) (in module pyrosetta.rosetta.protocols.loops) remove_cutpoint_variants_for_ccd() (in module pyrosetta.rosetta.protocols.grafting) remove_cutpoints() (in module pyrosetta.rosetta.protocols.forge.methods) remove_cutpoints_closed() (in module pyrosetta.rosetta.core.import_pose) remove_duplicates() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) remove_evaluation() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) remove_file() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) remove_from_string() (in module pyrosetta.rosetta.utility) remove_high_energy_water_molecules() (in module pyrosetta.rosetta.protocols.hydrate) remove_hotspot_constraints_from_pose() (in module pyrosetta.rosetta.protocols.hotspot_hashing) remove_last_filter() (pyrosetta.rosetta.protocols.filters.FilterCollection method) remove_ligand_canonical_residues() (in module pyrosetta.rosetta.core.pose) remove_lower_terminus_type_from_conformation_residue() (in module pyrosetta.rosetta.core.conformation) remove_lower_terminus_type_from_pose_residue() (in module pyrosetta.rosetta.core.pose) remove_mg_bound_waters() (in module pyrosetta.rosetta.protocols.magnesium) remove_missing_density() (in module pyrosetta.rosetta.protocols.loops) remove_missing_jump_atoms() (in module pyrosetta.rosetta.protocols.denovo_design) remove_models_from_dssp() (in module pyrosetta.rosetta.protocols.legacy_sewing) remove_non_buried_wat() (in module pyrosetta.rosetta.protocols.hydrate) remove_non_protein_residues() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) remove_nonbb_constraints() (in module pyrosetta.rosetta.core.scoring.constraints) remove_nonprotein_residues() (in module pyrosetta.rosetta.core.pose) remove_observer() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) remove_other_pose_at_idx() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) remove_register_shifts() (in module pyrosetta.rosetta.protocols.fldsgn.filters) remove_remark_header_for_geomcst() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) remove_remodel_constraints_from_pose() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) remove_residue_selector() (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) remove_short_chunks() (in module pyrosetta.rosetta.protocols.loops) remove_silent_file_if_it_exists() (in module pyrosetta.rosetta.core.io.silent) remove_singletons_and_update_pose_focus() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) remove_small_gaps() (in module pyrosetta.rosetta.protocols.loops) remove_terminal_loops() (pyrosetta.rosetta.protocols.loops.Loops method) remove_terminal_phosphates() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) remove_trigger() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) remove_unpatchable_residue_type() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) remove_upper_lower_variants_from_RNA() (in module pyrosetta.rosetta.core.pose.rna) remove_upper_terminus_type_from_conformation_residue() (in module pyrosetta.rosetta.core.conformation) remove_upper_terminus_type_from_pose_residue() (in module pyrosetta.rosetta.core.pose) remove_variant_type() (pyrosetta.rosetta.core.chemical.ResidueType method) remove_variant_type_from_conformation_residue() (in module pyrosetta.rosetta.core.conformation) remove_variant_type_from_pose_residue() (in module pyrosetta.rosetta.core.pose) remove_variant_type_from_residue() (in module pyrosetta.rosetta.core.pose) remove_virtual_O2Prime_hydrogen() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) remove_virtual_residues() (in module pyrosetta.rosetta.core.pose) remove_virtual_rna_residue_variant_type() (in module pyrosetta.rosetta.core.pose.rna) remove_waters_except_mg_bound() (in module pyrosetta.rosetta.protocols.magnesium) RemoveConstraints (class in pyrosetta.rosetta.protocols.constraint_generator) RemoveHybridization() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) RemoveNorCTermMPM (class in pyrosetta.rosetta.protocols.match) RemoveRotamerSpecifications (class in pyrosetta.rosetta.core.chemical) rename_atom() (pyrosetta.rosetta.core.io.ResidueInformation method) rename_atoms() (in module pyrosetta.rosetta.core.chemical) rename_energies() (pyrosetta.rosetta.core.io.silent.SilentStruct method) RenameAtom (class in pyrosetta.rosetta.core.chemical) renormalize_quota_pools() (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) renormalize_weights() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) renumber_after_variant_changes() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) renumber_all_decoys() (pyrosetta.rosetta.core.io.silent.SilentFileData method) renumber_jumps() (pyrosetta.rosetta.core.kinematics.FoldTree method) renumber_jumps_ordered() (pyrosetta.rosetta.core.kinematics.FoldTree method) renumber_pdb() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) renumber_pdbinfo_based_on_conf_chains() (in module pyrosetta.rosetta.core.pose) renumber_rotamers() (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) renumber_with_pdb_info() (in module pyrosetta.rosetta.protocols.hybridization) reorder() (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) reorder_foldtree_around_mobile_regions() (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) reorder_full_model_info_after_append() (in module pyrosetta.rosetta.core.pose.full_model_info) reorder_full_model_info_after_delete() (in module pyrosetta.rosetta.core.pose.full_model_info) reorder_full_model_info_after_prepend() (in module pyrosetta.rosetta.core.pose.full_model_info) reorder_glycan_residues() (in module pyrosetta.rosetta.core.io) reorder_membrane_foldtree() (in module pyrosetta.rosetta.protocols.membrane) reorder_pose() (in module pyrosetta.rosetta.core.import_pose) reorder_randomly() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) reorder_root_partition_res() (in module pyrosetta.rosetta.core.pose) reorder_with_first_non_mobile_as_root() (in module pyrosetta.rosetta.protocols.ligand_docking) reorient_extended_fibril() (in module pyrosetta.rosetta.protocols.fibril) rep_weight() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) repack() (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker method) repack_antibody_interface() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) repack_antigen_ab_interface() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) repack_antigen_interface() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) repack_cdrs() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) repack_chain1() (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) repack_chain2() (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) repack_connection_and_residues_in_movemap() (in module pyrosetta.rosetta.protocols.grafting) repack_connection_and_residues_in_movemap_and_piece() (in module pyrosetta.rosetta.protocols.grafting) repack_connection_and_residues_in_movemap_and_piece_and_neighbors() (in module pyrosetta.rosetta.protocols.grafting) repack_shell() (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) repack_these_residues() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) repack_this_residue() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) repackable_residues() (in module pyrosetta.rosetta.core.pack) repacking_residues() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) RepackingRefiner (class in pyrosetta.rosetta.protocols.loop_modeling.refiners) RepackLigandSiteWithoutLigandMover (class in pyrosetta.rosetta.protocols.enzdes) RepackMinimize (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) RepackSidechainsMover (class in pyrosetta.rosetta.protocols.minimization_packing) RepackTrialCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) repeat() (in module pyrosetta.rosetta.ObjexxFCL.format) repeat_generation_with_additional_residue() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) repeat_propagation() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) repeat_sync() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) repeat_to_preserve() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) repeating_unit_offset() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) RepeatMover (class in pyrosetta.rosetta.protocols.moves) repeats() (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) replace() (in module pyrosetta.rosetta.protocols.forge.methods) replace_atom() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) replace_conformation_residue_copying_existing_coordinates() (in module pyrosetta.rosetta.core.conformation) replace_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) replace_environment_variables() (in module pyrosetta.rosetta.utility) replace_file() (in module pyrosetta.rosetta.protocols.monte_carlo) replace_in() (in module pyrosetta.rosetta.utility) replace_option_namespace_colons_with_underscores() (in module pyrosetta.rosetta.basic.options) replace_pose_residue_copying_existing_coordinates() (in module pyrosetta.rosetta.core.pose) replace_region() (in module pyrosetta.rosetta.protocols.grafting) replace_res() (pyrosetta.rosetta.core.pose.PDBInfo method) replace_res_remap_bfactors() (pyrosetta.rosetta.core.pose.PDBInfo method) replace_residue() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) replace_residue_in_atom_tree() (in module pyrosetta.rosetta.core.conformation) replace_residue_keeping_all_atom_positions() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) replace_spaces() (in module pyrosetta.rosetta.utility) replace_tree() (pyrosetta.rosetta.core.kinematics.AtomTree method) replaced_symmetric_foldtree_with_new_monomer() (in module pyrosetta.rosetta.core.conformation.symmetry) ReplaceMainchainAtom (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithBromine (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithChlorine (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithEthyl (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithFluorine (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithHydroxyl (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithIodine (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithMethoxy (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithMethyl (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithTrifluoromethyl (class in pyrosetta.rosetta.core.chemical) ReplaceRegionMover (class in pyrosetta.rosetta.protocols.grafting.simple_movers) replaces() (pyrosetta.rosetta.core.chemical.Patch method) replaces_residue_type() (pyrosetta.rosetta.core.chemical.Patch method) Report (class in pyrosetta.rosetta.basic) report() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) report_ab_H3_kink_metrics_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) report_ab_metrics_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) report_adducts() (pyrosetta.rosetta.core.chemical.ResidueType method) report_all_interface_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) report_batch_inconsistency() (in module pyrosetta.rosetta.protocols.jd2.archive) report_binary_stats() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) report_CA_rmsd() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) report_cdr_metrics_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) report_cdr_residue_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) report_cdr_residue_features_row() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) report_crd() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) report_data() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) report_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) report_heading_directions_of_all_AA_in_a_strand() (in module pyrosetta.rosetta.protocols.features.strand_assembly) report_interface_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) report_interface_residue_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) report_interface_side_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) report_property() (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) report_ressolv() (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) report_rotamer_recovery() (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) report_sm() (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) report_subvalues() (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) report_unfolded() (in module pyrosetta.rosetta.protocols.fold_from_loops.utils) ReportEffectivePKA (class in pyrosetta.rosetta.protocols.simple_moves) Reporter (class in pyrosetta.rosetta.basic) ReportFSC (class in pyrosetta.rosetta.protocols.electron_density) ReportSequenceDifferences (class in pyrosetta.rosetta.protocols.protein_interface_design) represent_residue_selector() (in module pyrosetta.rosetta.core.select.residue_selector) representative_downstream_algorithm() (pyrosetta.rosetta.protocols.match.Matcher method) representative_group_matches() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) RepulsiveOnlyMover (class in pyrosetta.rosetta.protocols.simple_moves) request_data_from_head_node() (in module pyrosetta.rosetta.basic.mpi) request_fold_tree() (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) request_symmetrize_by_intersection() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) request_symmetrize_by_union() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) require_all_target_residue_atom_coordinates() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) require_candidate_residue_atoms_to_lie_near_target_atom() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) require_context_graph() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) require_final() (pyrosetta.rosetta.core.chemical.ResidueType method) require_mm_bend() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) require_target_atom_coordinate() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) required_attribute() (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) required_name_attribute() (in module pyrosetta.rosetta.utility.tag) requires_a_setup_for_derivatives_for_residue_opportunity() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) requires_a_setup_for_derivatives_for_residue_pair_opportunity() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) requires_a_setup_for_scoring_for_residue_opportunity_during_minimization() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) requires_a_setup_for_scoring_for_residue_pair_opportunity() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) requires_actcoord() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) requires_context_graph() (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) requires_pose() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) reroot() (in module pyrosetta.rosetta.core.pose) reroot_based_on_full_model_info() (in module pyrosetta.rosetta.protocols.stepwise.modeler) res() (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) res1() (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.RDC method) res2() (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.RDC method) res3() (pyrosetta.rosetta.core.scoring.CSA method) res_filter_schema_w_attributes() (in module pyrosetta.rosetta.core.pack.task.operation) res_haslabel() (pyrosetta.rosetta.core.pose.PDBInfo method) res_ids() (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) res_in_chain() (in module pyrosetta.rosetta.core.pose) res_is_mirrored() (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) res_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) res_lvl_task_op_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.ResLvlTaskOperationLoader method) res_lvl_task_op_schema_empty() (in module pyrosetta.rosetta.core.pack.task.operation) res_lvl_task_op_schema_w_attributes() (in module pyrosetta.rosetta.core.pack.task.operation) res_min_data() (pyrosetta.rosetta.core.scoring.MinimizationNode method) res_moved() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) res_name() (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) res_name1() (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) res_name2() (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) res_num() (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) res_pair_min_data() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) res_res_min_distance() (in module pyrosetta.rosetta.protocols.simple_filters) res_res_weight() (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer method) res_rmsd() (in module pyrosetta.rosetta.protocols.protein_interface_design.filters) res_selector_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader method) resA() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) resB() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) rescale_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) ResConnID (class in pyrosetta.rosetta.core.chemical) rescore() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) rescore_fragment_crmsd() (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) reserve() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) reserve_buffers() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) reserve_destination_size() (pyrosetta.rosetta.utility.subset_mapping method) reservoir_sample_accept_prob() (in module pyrosetta.rosetta.numeric.random) RESET (class in pyrosetta.rosetta.core.pack.task) reset() (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup method) Reset() (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) reset() (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.checkpoint.Timer method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) reset_3d_projection() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) reset_accept_counter() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) reset_accounting() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) reset_arrays_danger_expert_only() (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase method) reset_base_type_cop() (pyrosetta.rosetta.core.chemical.ResidueType method) reset_baseline() (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) reset_baselines() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) reset_bond_distance_to_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) reset_chain_endings() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) reset_count() (pyrosetta.rosetta.protocols.contact_map.Contact method) reset_counters() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) reset_counts() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) reset_cycle_index() (pyrosetta.rosetta.protocols.moves.CycleMover method) reset_delta_omega1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) reset_delta_z1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) reset_edge_list_iterator_for_node() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) reset_energy_methods() (pyrosetta.rosetta.core.scoring.ScoreFunction method) reset_filters() (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) reset_jump_rb_deltas() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) reset_mainchain_torsion_potential_names() (pyrosetta.rosetta.core.chemical.ResidueType method) reset_mode() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) reset_move_data() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) reset_nblist() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) reset_num_connections() (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) reset_r1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) reset_recovery() (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) reset_res_moved() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) reset_residue_list() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) reset_residue_type_set_for_conf() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) reset_rpe_calculations_count() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) reset_sample_index() (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) reset_scorefxn() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) reset_status() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) reset_structure_moved() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) reset_surface_residue_information() (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) reset_task_factory() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) reset_timer() (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) reset_x() (in module pyrosetta.rosetta.protocols.toolbox) ResetBondLength (class in pyrosetta.rosetta.core.chemical) resfile() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) resfile_commands() (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) ResfileCommand (class in pyrosetta.rosetta.core.pack.task) ResfileCommandOperation (class in pyrosetta.rosetta.protocols.task_operations) ResFilterCreator (class in pyrosetta.rosetta.core.pack.task.operation) ResHasher (class in pyrosetta.rosetta.protocols.mean_field) ResHashMap (class in pyrosetta.rosetta.protocols.mean_field) resi() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) ResId (class in pyrosetta.rosetta.protocols.moves) resid() (pyrosetta.rosetta.core.chemical.ResConnID method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) residual_squared_of_points_to_plane() (in module pyrosetta.rosetta.numeric.geometry) ResidualDipolarCoupling (class in pyrosetta.rosetta.core.scoring) ResidualDipolarCouplingRigidSegments (class in pyrosetta.rosetta.protocols.scoring) Residue (class in pyrosetta.rosetta.core.conformation) (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover) residue() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc method) (pyrosetta.rosetta.core.scoring.func.XYZ_Func method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) residue_action() (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AROMATIC method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.CHARGED method) (pyrosetta.rosetta.core.pack.task.EMPTY method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NC method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.PIKRNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PROPERTY method) (pyrosetta.rosetta.core.pack.task.RESET method) (pyrosetta.rosetta.core.pack.task.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) residue_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) residue_atomtree_collection() (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection method) residue_atomtree_collection_op() (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection method) residue_base2_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) residue_base_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) residue_center_of_mass() (in module pyrosetta.rosetta.core.conformation.symmetry) (in module pyrosetta.rosetta.core.pose) residue_conformations_redundant() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) residue_connect_atom_index() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) residue_connection() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) residue_connection_conn_id() (pyrosetta.rosetta.core.conformation.Residue method) residue_connection_id_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) residue_connection_is_polymeric() (pyrosetta.rosetta.core.chemical.ResidueType method) residue_connection_partner() (pyrosetta.rosetta.core.conformation.Residue method) residue_connections_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) residue_cop() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) residue_data() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) residue_derivatives() (pyrosetta.rosetta.core.scoring.GenericBondedPotential method) residue_energy() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.GenericBondedPotential method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) residue_energy_ext() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) residue_gws_string() (in module pyrosetta.rosetta.core.io.carbohydrates) residue_hbonds() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) residue_index() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) residue_info() (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) residue_is_floppy() (in module pyrosetta.rosetta.protocols.sic_dock) residue_is_in_fold_tree() (pyrosetta.rosetta.core.kinematics.FoldTree method) residue_is_surface() (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) residue_iterated_on() (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) residue_list() (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) residue_near_water() (in module pyrosetta.rosetta.core.scoring.hbonds) (in module pyrosetta.rosetta.protocols.hydrate) residue_neighbors_updated() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) residue_num() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) residue_number_string() (in module pyrosetta.rosetta.utility.tag) residue_numbers_into_pose() (pyrosetta.rosetta.core.io.silent.SilentStruct method) residue_packed() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) residue_packer_states() (in module pyrosetta.rosetta.protocols.rosetta_scripts) residue_pair_constraint_exists() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) residue_pair_constraints_begin() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) residue_pair_constraints_end() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) residue_pair_constraints_exists() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) residue_pair_derivatives() (pyrosetta.rosetta.core.scoring.GenericBondedPotential method) residue_pair_energy() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.GenericBondedPotential method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) residue_pair_energy_ext() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) residue_pairs() (in module pyrosetta.bindings.pose) (pyrosetta.rosetta.core.pose.Pose method) residue_point_graph_from_conformation() (in module pyrosetta.rosetta.core.conformation) residue_position() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) residue_range_gws_string() (in module pyrosetta.rosetta.core.io.carbohydrates) residue_rotamer_recovery() (in module pyrosetta.rosetta.core.pack) residue_sc_rmsd_no_super() (in module pyrosetta.rosetta.core.scoring) (in module pyrosetta.rosetta.protocols.hotspot_hashing) residue_selector() (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) residue_selector_single_from_line() (in module pyrosetta.rosetta.core.chemical) residue_subset() (in module pyrosetta.rosetta.protocols.pose_metric_calculators) residue_task() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) residue_total_energies() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) residue_total_energy() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) residue_type() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) residue_type_all_patches_name() (in module pyrosetta.rosetta.core.chemical) residue_type_base_name() (in module pyrosetta.rosetta.core.chemical) residue_type_base_names() (pyrosetta.rosetta.core.io.StructFileRep method) residue_type_ptr() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) residue_type_set() (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) residue_type_set_for_conf() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) residue_type_set_for_pose() (pyrosetta.rosetta.core.pose.Pose method) residue_type_set_mode() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) residue_types_from_saccharide_sequence() (in module pyrosetta.rosetta.core.pose) residue_types_from_sequence() (in module pyrosetta.rosetta.core.pose) residue_typeset_mode() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) residue_xyz_change_list_begin() (pyrosetta.rosetta.core.kinematics.AtomTree method) residue_xyz_change_list_end() (pyrosetta.rosetta.core.kinematics.AtomTree method) residue_z_position() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) ResidueAtomTreeCollection (class in pyrosetta.rosetta.core.pack.scmin) ResidueAtomTreeCollectionMomento (class in pyrosetta.rosetta.core.pack.scmin) ResidueBurialFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueChainVectorOption (class in pyrosetta.rosetta.utility.options) ResidueChainVectorOptionKey (class in pyrosetta.rosetta.utility.options) ResidueConformationFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueConformerFilter (class in pyrosetta.rosetta.protocols.enzdes) ResidueConnection (class in pyrosetta.rosetta.core.chemical) ResidueConstraints (class in pyrosetta.rosetta.core.scoring.constraints) ResidueCoordinateChangeList (class in pyrosetta.rosetta.core.kinematics) ResidueDataCacheIndex (class in pyrosetta.rosetta.core.conformation.residue_datacache) ResidueDepthCalculator (class in pyrosetta.rosetta.protocols.simple_filters) ResidueDepthData (class in pyrosetta.rosetta.protocols.simple_filters) ResidueDepthFilter (class in pyrosetta.rosetta.protocols.simple_filters) ResidueElement (class in pyrosetta.rosetta.protocols.environment.claims) ResidueFactory (class in pyrosetta.rosetta.core.conformation) ResidueFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueGridScoresFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueHasProperty (class in pyrosetta.rosetta.core.pack.task.operation) ResidueIdentifier (class in pyrosetta.rosetta.protocols.loops) ResidueIndexDescription (class in pyrosetta.rosetta.core.pose) ResidueIndexDescriptionFromFile (class in pyrosetta.rosetta.core.pose) ResidueIndexSelector (class in pyrosetta.rosetta.core.select.residue_selector) ResidueInformation (class in pyrosetta.rosetta.core.io) ResidueInMembraneSelector (class in pyrosetta.rosetta.core.select.residue_selector) ResidueInSequenceMotifSelector (class in pyrosetta.rosetta.core.select.residue_selector) ResidueLabelsToPymolSelectionMover (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) ResidueLevelTask_ (class in pyrosetta.rosetta.core.pack.task) ResidueNameSelector (class in pyrosetta.rosetta.core.select.residue_selector) ResidueNetwork (class in pyrosetta.rosetta.protocols.toolbox) ResiduePairEvalType (class in pyrosetta.rosetta.core.pack.interaction_graph) ResiduePairJumpSetup (class in pyrosetta.rosetta.protocols.jumping) ResiduePairJumpSingle (class in pyrosetta.rosetta.protocols.jumping) ResiduePDBInfoHasLabelSelector (class in pyrosetta.rosetta.core.select.residue_selector) ResidueProbDesignOperation (class in pyrosetta.rosetta.protocols.task_operations) ResidueProperties (class in pyrosetta.rosetta.core.chemical) ResidueProperty (class in pyrosetta.rosetta.core.chemical) ResidueRange (class in pyrosetta.rosetta.core.select.residue_selector) residues() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) residues_downstream_of_jump() (in module pyrosetta.rosetta.core.kinematics) residues_for_atom_name_remapping() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) residues_interact() (in module pyrosetta.rosetta.core.scoring.methods) residues_moved_begin() (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) residues_moved_end() (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) residues_per_repeat() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) residues_upstream_of_jump() (in module pyrosetta.rosetta.core.kinematics) ResidueScoresFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueSecondaryStructureFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueSelectorLoader (class in pyrosetta.rosetta.protocols.parser) ResidueSpanSelector (class in pyrosetta.rosetta.core.select.residue_selector) ResidueTorsionRestraints (class in pyrosetta.rosetta.protocols.ligand_docking) ResidueTotalScoresFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueType (class in pyrosetta.rosetta.core.chemical) residueType() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) ResidueTypeConstraint (class in pyrosetta.rosetta.core.scoring.constraints) ResidueTypeConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) ResidueTypeLinkingConstraint (class in pyrosetta.rosetta.core.scoring.constraints) ResidueTypeSelector (class in pyrosetta.rosetta.core.chemical) ResidueTypeSelectorSingle (class in pyrosetta.rosetta.core.chemical) ResidueTypeSet (class in pyrosetta.rosetta.core.chemical) ResidueTypesFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueVicinityInfo (class in pyrosetta.rosetta.protocols.forge.remodel) ResidueVicinityRCG (class in pyrosetta.rosetta.protocols.forge.remodel) resindex() (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) resize() (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.core.scoring.Helices method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.Strands method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) resize_atom_records() (pyrosetta.rosetta.core.pose.PDBInfo method) resize_bb_donor_acceptor_arrays() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) resize_residue_records() (pyrosetta.rosetta.core.pose.PDBInfo method) ResLvlTaskOperationCreator (class in pyrosetta.rosetta.core.pack.task.operation) ResLvlTaskOperationLoader (class in pyrosetta.rosetta.protocols.parser) resName() (pyrosetta.rosetta.core.io.ResidueInformation method) resname() (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) resnum() (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) resnum_and_chain() (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) resnum_exists_in_set() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) resolution() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) resolve_db_partition() (in module pyrosetta.rosetta.basic.database) resolve_index() (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) resolve_loop_indices() (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) resolve_loop_indices_once() (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) Resonance (class in pyrosetta.rosetta.protocols.noesy_assign) resonance() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) resonance_id() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) ResonanceList (class in pyrosetta.rosetta.protocols.noesy_assign) resonances() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) resonances_at_residue() (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) resource_definition_xsd() (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) resource_loader_xsd_type_definition_w_attributes() (in module pyrosetta.rosetta.basic.resource_manager) resource_loader_xsd_type_definition_w_attributes_and_repeatable_subelements() (in module pyrosetta.rosetta.basic.resource_manager) ResourceLoader (class in pyrosetta.rosetta.basic.resource_manager) ResourceLoaderCreator (class in pyrosetta.rosetta.basic.resource_manager) ResourceLoaderFactory (class in pyrosetta.rosetta.basic.resource_manager) ResourceLocator (class in pyrosetta.rosetta.basic.resource_manager) ResourceLocatorCreator (class in pyrosetta.rosetta.basic.resource_manager) ResourceLocatorFactory (class in pyrosetta.rosetta.basic.resource_manager) ResourceManagerCreator (class in pyrosetta.rosetta.basic.resource_manager) ResourceManagerFactory (class in pyrosetta.rosetta.basic.resource_manager) ResourceStream (class in pyrosetta.rosetta.basic.resource_manager) respect_this_movemap() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) respond_to_peripheral_hitlist_change() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) respond_to_primary_hitlist_change() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) ResPred (class in pyrosetta.rosetta.protocols.mean_field) ResRangePredicate (class in pyrosetta.rosetta.core.scoring) resSeq() (pyrosetta.rosetta.core.io.ResidueInformation method) restart() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) restart_mode() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) restart_simulation() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) restore() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) restore_archive() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) restore_from_file() (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) restore_pose_from_rbsegs() (in module pyrosetta.rosetta.protocols.rbsegment_relax) restore_residues() (in module pyrosetta.rosetta.protocols.forge.methods) restore_status() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) restoreState() (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) restrain_ligand_nbr_atom() (in module pyrosetta.rosetta.protocols.ligand_docking) restrain_protein_Calphas() (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) restrict_absent_canonical_aas() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) restrict_absent_nas() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) restrict_access() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) restrict_identities() (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) restrict_non_nbrs_from_repacking() (in module pyrosetta.toolbox) restrict_nonnative_canonical_aas() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) restrict_only_design_to_loops() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) restrict_prec() (in module pyrosetta.rosetta.core.io.pose_to_sfr) restrict_sequence_profile() (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) restrict_to_aligned_segments() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) restrict_to_canonical_aas() (in module pyrosetta.rosetta.protocols.multistate_design) restrict_to_protein_residues() (in module pyrosetta.rosetta.protocols.ligand_docking) restrict_to_repacking() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) restrict_to_residue() (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) restrict_to_residues() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) restrict_to_single_sequence() (in module pyrosetta.rosetta.protocols.dna) RestrictByCalculatorsOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictChainToRepackingOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictConservedLowDdgOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictIdentitiesAtAlignedPositionsOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictIdentitiesOperation (class in pyrosetta.rosetta.protocols.task_operations) restriction_type_name() (in module pyrosetta.rosetta.utility.tag) RestrictNonSurfaceToRepackingOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictOperationsBase (class in pyrosetta.rosetta.protocols.task_operations) RestrictResiduesToRepackingOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictResidueToRepacking (class in pyrosetta.rosetta.core.pack.task.operation) RestrictToAlignedSegmentsOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictToCDRsAndNeighbors (class in pyrosetta.rosetta.protocols.antibody.task_operations) RestrictToInterfaceOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictToInterfaceVectorOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictToLoopsAndNeighbors (class in pyrosetta.rosetta.protocols.simple_task_operations) RestrictToMoveMapChiOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictToNeighborhoodOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictYSDesign (class in pyrosetta.rosetta.core.pack.task.operation) restype() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) restype_char() (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) restype_destruction_observer() (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap method) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) restype_geometry() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) restype_index() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) RestypeDestructionEvent (class in pyrosetta.rosetta.core.chemical) restypeinfo() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) result_id() (pyrosetta.rosetta.protocols.jd3.output.OutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification method) result_outputter() (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) result_sizes() (in module pyrosetta.rosetta.protocols.antibody.grafting) ResultOutputter (class in pyrosetta.rosetta.protocols.jd3.output) retain_top() (in module pyrosetta.rosetta.core.fragment) retrieve_base_partner_from_pose() (in module pyrosetta.rosetta.core.scoring.dna) retrieve_bulges() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) retrieve_bulges_s() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) retrieve_centroid_scatter_from_pose() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) retrieve_connection_architect() (in module pyrosetta.rosetta.protocols.denovo_design.connection) retrieve_constraints() (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) retrieve_CSA_from_pose() (in module pyrosetta.rosetta.core.scoring) retrieve_DC_from_pose() (in module pyrosetta.rosetta.core.scoring) retrieve_denovo_architect() (in module pyrosetta.rosetta.protocols.denovo_design.architects) retrieve_energy() (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) retrieve_fa_scatter_from_pose() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) retrieve_lengths() (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) retrieve_observer() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) retrieve_RDC_from_pose() (in module pyrosetta.rosetta.core.scoring) retrieve_RDC_ROHL_from_pose() (in module pyrosetta.rosetta.core.scoring) retrieve_RDC_segments_from_pose() (in module pyrosetta.rosetta.protocols.scoring) retrieve_register_shifts() (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) retrieve_residue_num_of_rkde() (in module pyrosetta.rosetta.protocols.features.strand_assembly) RetrieveStoredTaskOperation (class in pyrosetta.rosetta.protocols.task_operations) retry_limit() (pyrosetta.rosetta.protocols.jd3.LarvalJob method) return_centroid() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) return_hbond_to_queue() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) return_key() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) return_nearest_residue() (in module pyrosetta.rosetta.core.conformation.symmetry) (in module pyrosetta.rosetta.core.pose) return_region() (in module pyrosetta.rosetta.protocols.grafting) ReturnResidueSubsetSelector (class in pyrosetta.rosetta.core.select.residue_selector) ReturnSidechainMover (class in pyrosetta.rosetta.protocols.simple_moves) reverse() (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) reverse_chains() (in module pyrosetta.rosetta.protocols.denovo_design.components) reverse_connections() (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) reverse_lengths() (in module pyrosetta.rosetta.protocols.denovo_design.components) reverse_orientations() (in module pyrosetta.rosetta.protocols.denovo_design.components) reverse_score_filter() (pyrosetta.rosetta.core.io.silent.SilentFileData method) reversed() (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.kinematics.Jump method) Revert (class in pyrosetta.rosetta.protocols.protein_interface_design) revert_to_pre_talaris_2013_defaults() (in module pyrosetta.rosetta.core.init) revise_root_and_moving_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) revise_root_and_moving_res_list() (in module pyrosetta.rosetta.protocols.stepwise.modeler) revision_id() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) reweighters_begin() (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer method) reweighters_end() (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer method) rg() (in module pyrosetta.rosetta.numeric.random) rgb_to_hsv() (in module pyrosetta.rosetta.numeric) right_justified() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) right_justify() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) right_string_of() (in module pyrosetta.rosetta.ObjexxFCL) right_stub_atoms() (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) rigid_body_move() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) rigid_transform_3D() (in module pyrosetta.toolbox.numpy_utils) RigidBodyDofPerturbMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyDofRandomizeMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyDofRandomTransMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyDofSeqPerturbMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyDofSeqRandomizeMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyDofSeqTransMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyDofTransMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyMoveBaseRSO (class in pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations) RigidBodyMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyMoveRSO (class in pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations) RigidBodyPerturbMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyPerturbNoCenterMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodySilentStructCreator (class in pyrosetta.rosetta.core.io.silent) RigidBodySpinMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyTiltMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyTransMover (class in pyrosetta.rosetta.protocols.rigid) RigidChunkClaimer (class in pyrosetta.rosetta.protocols.topology_broker) RigidSearchMover (class in pyrosetta.rosetta.protocols.ligand_docking) ring_affix_from_ring_size() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) ring_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) ring_conformer() (pyrosetta.rosetta.core.conformation.Residue method) ring_conformer_set() (pyrosetta.rosetta.core.chemical.ResidueType method) ring_current_coeff() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) ring_current_effect() (in module pyrosetta.rosetta.core.scoring.rna.chemical_shift) ring_height() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) ring_intensity() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) ring_pos() (in module pyrosetta.rosetta.core.scoring.rna.chemical_shift) ring_radius() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) RingConformationMover (class in pyrosetta.rosetta.protocols.simple_moves) RingConformationMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) RingConformer (class in pyrosetta.rosetta.core.chemical.rings) RingConformerManager (class in pyrosetta.rosetta.core.chemical.rings) ringness() (pyrosetta.rosetta.core.chemical.Bond method) rjust() (in module pyrosetta.rosetta.ObjexxFCL) rKirkwood() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) rlto_datamap_category() (in module pyrosetta.rosetta.core.pack.task.operation) RM_Type (class in pyrosetta.rosetta.core.scoring.motif) rm_virt_phosphate() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) rms_at_all_corresponding_atoms() (in module pyrosetta.rosetta.core.scoring) rms_at_corresponding_atoms() (in module pyrosetta.rosetta.core.scoring) rms_at_corresponding_atoms_no_super() (in module pyrosetta.rosetta.core.scoring) rms_at_corresponding_heavy_atoms() (in module pyrosetta.rosetta.core.scoring) rms_error_with_noise() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) rms_fit() (in module pyrosetta.rosetta.numeric.model_quality) rms_pose_list() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) rms_wrapper() (in module pyrosetta.rosetta.numeric.model_quality) rms_wrapper_slow_and_correct() (in module pyrosetta.rosetta.numeric.model_quality) RMSD() (in module pyrosetta.rosetta.protocols.cluster.calibur) rmsd() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) rmsd_atoms (class in pyrosetta.rosetta.protocols.analysis.simple_metrics) rmsd_over_residue_list() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) rmsd_screen() (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) RmsData (class in pyrosetta.rosetta.numeric.model_quality) RmsdEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) RMSDMetric (class in pyrosetta.rosetta.protocols.analysis.simple_metrics) RMSDReporter (class in pyrosetta.rosetta.protocols.pose_reporters) RmsdTargetEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) rmsfitca3() (in module pyrosetta.rosetta.numeric.model_quality) RMSwrapper() (in module pyrosetta.rosetta.protocols.simple_filters) RNA_AddDeleteMonteCarlo (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna) RNA_AnalyticLoopCloser (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) rna_anti_chi_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) rna_backbone_backbone_pair_energy() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) RNA_base_atoms() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) rna_base_backbone_pair_energy() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) rna_block_stack_above_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) rna_block_stack_below_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) rna_bulge_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) rna_centroid_info() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) RNA_CentroidInfo (class in pyrosetta.rosetta.core.scoring.rna) RNA_ChemicalShiftEnergy (class in pyrosetta.rosetta.core.scoring.rna.chemical_shift) RNA_ChunkLibrary (class in pyrosetta.rosetta.core.import_pose.libraries) RNA_CS_parameters (class in pyrosetta.rosetta.core.scoring.rna.chemical_shift) RNA_CS_residue_parameters (class in pyrosetta.rosetta.core.scoring.rna.chemical_shift) rna_data() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) rna_data_info() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) RNA_DataInfo (class in pyrosetta.rosetta.core.pose.rna) RNA_DataReader (class in pyrosetta.rosetta.core.io.rna) RNA_DeNovoPoseInitializer (class in pyrosetta.rosetta.protocols.rna.denovo) RNA_DeNovoProtocol (class in pyrosetta.rosetta.protocols.rna.denovo) rna_dna_match() (in module pyrosetta.rosetta.core.chemical.rna) rna_filtered_base_base_info() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) RNA_FilteredBaseBaseInfo (class in pyrosetta.rosetta.core.pose.rna) RNA_FittedTorsionInfo (class in pyrosetta.rosetta.core.chemical.rna) rna_fragment_library() (pyrosetta.rosetta.core.import_pose.libraries.RNA_LibraryManager method) rna_fragment_monte_carlo() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) RNA_FragmentMover (class in pyrosetta.rosetta.protocols.rna.denovo.movers) RNA_HelixAssembler (class in pyrosetta.rosetta.core.import_pose) RNA_HelixMover (class in pyrosetta.rosetta.protocols.rna.denovo.movers) RNA_Info (class in pyrosetta.rosetta.core.chemical.rna) RNA_info() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) rna_jump_library() (pyrosetta.rosetta.core.import_pose.libraries.RNA_LibraryManager method) rna_jump_library_cop() (pyrosetta.rosetta.core.import_pose.libraries.RNA_LibraryManager method) RNA_JumpLibrary (class in pyrosetta.rosetta.core.import_pose.libraries) RNA_KinematicCloser (class in pyrosetta.rosetta.protocols.stepwise.sampler.rna) rna_legacy_output_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) RNA_LibraryManager (class in pyrosetta.rosetta.core.import_pose.libraries) RNA_LoopCloser (class in pyrosetta.rosetta.protocols.rna.movers) RNA_LowResolutionPotential (class in pyrosetta.rosetta.core.scoring.rna) RNA_Minimizer (class in pyrosetta.rosetta.protocols.rna.denovo.movers) RNA_MotifType (class in pyrosetta.rosetta.core.scoring.rna) RNA_O2PrimeMover (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna) rna_options() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) RNA_PairingTemplate (class in pyrosetta.rosetta.core.import_pose.libraries) rna_params() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) rna_raw_base_base_info() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) RNA_RawBaseBaseInfo (class in pyrosetta.rosetta.core.pose.rna) rna_reactivities() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) RNA_ReactivityType (class in pyrosetta.rosetta.core.pose.rna) RNA_Relaxer (class in pyrosetta.rosetta.protocols.rna.denovo.movers) rna_repulsive_pair_energy() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) rna_residue_name_to_num() (in module pyrosetta.rosetta.core.scoring.rna) rna_sample_sugar_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) rna_scoring_info_from_pose() (in module pyrosetta.rosetta.core.scoring.rna) RNA_ScoringInfo (class in pyrosetta.rosetta.core.scoring.rna) RNA_SecStructLegacyInfo (class in pyrosetta.rosetta.core.pose.rna.secstruct_legacy) RNA_SilentStructCreator (class in pyrosetta.rosetta.core.io.silent) RNA_SuiteAssignment (class in pyrosetta.rosetta.core.pose.rna) RNA_SuiteInfo (class in pyrosetta.rosetta.core.pose.rna) RNA_SuiteName (class in pyrosetta.rosetta.core.pose.rna) rna_syn_chi_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) rna_task() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) rna_terminal_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) RNA_Torsion (class in pyrosetta.rosetta.core.chemical.rna) RNA_TorsionMover (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna) rna_update_last_controlling_chi() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) RNAAtomType (class in pyrosetta.rosetta) RNAIdealizeMover (class in pyrosetta.rosetta.protocols.rna.movers) RNAThreadAndMinimizeMover (class in pyrosetta.rosetta.protocols.rna.movers) rnl_pose() (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) RNP_HighResMover (class in pyrosetta.rosetta.protocols.rna.denovo.movers) RNP_LowResPairDistPotential (class in pyrosetta.rosetta.core.scoring.rna) RNP_LowResPotential (class in pyrosetta.rosetta.core.scoring.rna) RocStatus (class in pyrosetta.rosetta.numeric) rolling_score() (in module pyrosetta.rosetta.protocols.frag_picker.scores) root() (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) root_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) root_expression() (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) root_from_code() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) rootj() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) rosetta_names_from_pdb_code() (pyrosetta.rosetta.core.io.NomenclatureManager method) rosetta_recharge_fullatom() (in module pyrosetta.rosetta.core.chemical) rosetta_res_type() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) rosetta_resName() (pyrosetta.rosetta.core.io.ResidueInformation method) rosetta_retype_fullatom() (in module pyrosetta.rosetta.core.chemical) rosetta_scripts_complex_type_naming_func() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) rosetta_scripts_element_name() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) RosettaModuleOptionType (class in pyrosetta.rosetta.utility.xsd_util) RosettaModuleType (class in pyrosetta.rosetta.utility.xsd_util) RosettaScriptsParser (class in pyrosetta.rosetta.protocols.rosetta_scripts) rot_center() (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) rot_ind() (pyrosetta.rosetta.protocols.mean_field.RotProb method) rot_magnitude() (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) rot_matrices() (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) rot_matrix() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) rot_pose() (in module pyrosetta.rosetta.protocols.sic_dock) rot_sample_from_name() (in module pyrosetta.rosetta.core.pack.task) rotamer() (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) rotamer_aa() (pyrosetta.rosetta.core.chemical.ResidueType method) rotamer_couplings() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) rotamer_couplings_exist() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) rotamer_data_cache() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) rotamer_energy() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) rotamer_energy_deriv() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) rotamer_from_chi() (in module pyrosetta.rosetta.core.pack.dunbrack) rotamer_from_chi_02() (in module pyrosetta.rosetta.core.pack.dunbrack) rotamer_index() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) rotamer_information_from_PDB_stream() (in module pyrosetta.rosetta.core.pack.rotamers) rotamer_library() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) rotamer_library_specification() (pyrosetta.rosetta.core.chemical.ResidueType method) rotamer_library_specification_nonconst() (pyrosetta.rosetta.core.chemical.ResidueType method) rotamer_links() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) rotamer_links_exist() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) rotamer_operations() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) rotamer_recovery() (in module pyrosetta.rosetta.core.pack) rotamer_ref() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) rotamer_sampling_data_xml_schema_attributes() (in module pyrosetta.rosetta.core.pack.task.operation) rotamer_set_contains_rotamer() (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) rotamer_set_operation_begin() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) rotamer_set_operation_end() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) rotamer_sets() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) rotamer_trials() (in module pyrosetta.rosetta.core.pack) RotamerBoltzmannWeight2 (class in pyrosetta.rosetta.protocols.calc_taskop_filters) RotamerBoltzmannWeight2.ScoreType (class in pyrosetta.rosetta.protocols.calc_taskop_filters) RotamerBoltzmannWeightEvaluator (class in pyrosetta.rosetta.protocols.toolbox) RotamerBoltzmannWeightFeaturesCreator (class in pyrosetta.rosetta.protocols.features) RotamerBuildingData (class in pyrosetta.rosetta.core.pack.dunbrack) RotamerConstraint (class in pyrosetta.rosetta.core.pack.dunbrack) RotamerDots (class in pyrosetta.rosetta.core.pack.interaction_graph) RotamerDotsCache (class in pyrosetta.rosetta.core.pack.interaction_graph) RotamerDotsRadiusData (class in pyrosetta.rosetta.core.pack.interaction_graph) RotamerDumpMover (class in pyrosetta.rosetta.protocols.RotamerDump) RotamerExplosion (class in pyrosetta.rosetta.core.pack.task.operation) RotamerFeaturesCreator (class in pyrosetta.rosetta.protocols.features) RotamericSingleResidueDunbrackLibraryParser (class in pyrosetta.rosetta.core.pack.dunbrack) RotamerizeMover (class in pyrosetta.rosetta.protocols.minimization_packing) RotamerLibrary (class in pyrosetta.rosetta.core.pack.dunbrack) RotamerOperation (class in pyrosetta.rosetta.core.pack.rotamer_set) RotamerRecoveryFactory (class in pyrosetta.rosetta.protocols.rotamer_recovery) RotamerRecoveryFeaturesCreator (class in pyrosetta.rosetta.protocols.features) rotamers_for_trials() (in module pyrosetta.rosetta.protocols.ligand_docking) RotamerSet_ (class in pyrosetta.rosetta.core.pack.rotamer_set) RotamerSubset (class in pyrosetta.rosetta.core.pack.rotamer_set) RotamerTrialsRefiner (class in pyrosetta.rosetta.protocols.loop_modeling.refiners) rotate() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) rotate_anchor_to_x_axis() (in module pyrosetta.rosetta.core.pose.symmetry) rotate_around_atom() (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) rotate_around_downstream_centroid() (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) rotate_into_nucleobase_frame() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) rotate_into_phosphate_frame() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) rotate_pose() (in module pyrosetta.toolbox.numpy_utils) rotate_segment() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) RotateJumpAxisMover (class in pyrosetta.rosetta.protocols.rigid) RotateSegmentMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) rotation() (pyrosetta.rosetta.core.kinematics.Stub method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) rotation_axis() (in module pyrosetta.rosetta.numeric) rotation_by_axis() (pyrosetta.rosetta.core.kinematics.Jump method) rotation_by_matrix() (pyrosetta.rosetta.core.kinematics.Jump method) rotation_matrix() (in module pyrosetta.rosetta.numeric) RotationMover (class in pyrosetta.rosetta.protocols.membrane) RotationMoverCreator (class in pyrosetta.rosetta.protocols.membrane) RotMatrix (class in pyrosetta.rosetta.protocols.mean_field) RotProb (class in pyrosetta.rosetta.protocols.mean_field) round() (in module pyrosetta.rosetta.utility) round_to_float() (in module pyrosetta.rosetta.protocols.features.strand_assembly) round_to_Real() (in module pyrosetta.rosetta.protocols.features.strand_assembly) round_to_Size() (in module pyrosetta.rosetta.protocols.features.strand_assembly) rpad() (in module pyrosetta.rosetta.ObjexxFCL) rpadded() (in module pyrosetta.rosetta.ObjexxFCL) RPM_Type (class in pyrosetta.rosetta.core.scoring.motif) rpm_type1() (in module pyrosetta.rosetta.core.scoring.motif) rpm_type2() (in module pyrosetta.rosetta.core.scoring.motif) rrange() (in module pyrosetta) RRComparer (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRComparerCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRProtocol (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRProtocolCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRReporter (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRReporterCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRReporterHuman (class in pyrosetta.rosetta.protocols.rotamer_recovery) rsd() (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.scoring.AtomNeighbor method) rsd1() (pyrosetta.rosetta.core.id.JumpID method) rsd2() (pyrosetta.rosetta.core.id.JumpID method) rsd_closest_to_chain_com() (in module pyrosetta.rosetta.protocols.membrane) rsd_closest_to_chain_tm_com() (in module pyrosetta.rosetta.protocols.membrane) rsd_closest_to_pose_tm_com() (in module pyrosetta.rosetta.protocols.membrane) rsd_rsd_energy() (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential method) rsd_set_from_cmd_line() (in module pyrosetta.rosetta.core.chemical) rsigma_dot_initializer() (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential method) rstrip() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) rstrip_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) rstripped() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) rstripped_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) rswitch() (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) rt() (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) rt_min() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) run() (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.CartesianMinimizer method) (pyrosetta.rosetta.core.optimization.Minimizer method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.jd3.Job method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) run_boinc_debug() (in module pyrosetta.rosetta.protocols.abinitio) run_command() (in module pyrosetta.rosetta.protocols.frag_picker) RunSimpleMetricsMover (class in pyrosetta.rosetta.protocols.analysis.simple_metrics)

S

s() (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering method) (pyrosetta.rosetta.utility.py.Value method) s1_end() (pyrosetta.rosetta.core.scoring.Hairpin method) s1_start() (pyrosetta.rosetta.core.scoring.Hairpin method) s2_end() (pyrosetta.rosetta.core.scoring.Hairpin method) s2_start() (pyrosetta.rosetta.core.scoring.Hairpin method) s2d() (pyrosetta.rosetta.utility.subset_mapping method) sa() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) sa_faraggi_max() (in module pyrosetta.rosetta.protocols.frag_picker) sa_norm() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) safe() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) safe_read() (in module pyrosetta.rosetta.core.chemical.gasteiger) safe_secstruct() (in module pyrosetta.rosetta.protocols.jumping) safe_segment() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) safe_set_extended_torsions_and_idealize_loops() (in module pyrosetta.rosetta.protocols.loops) safe_write() (in module pyrosetta.rosetta.core.chemical.gasteiger) safely_append_polymer_residue_after_seqpos() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) safely_prepare_statement() (in module pyrosetta.rosetta.basic.database) safely_prepend_polymer_residue_before_seqpos() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) safely_read_from_database() (in module pyrosetta.rosetta.basic.database) safely_write_to_database() (in module pyrosetta.rosetta.basic.database) SaltBridgeFeaturesCreator (class in pyrosetta.rosetta.protocols.features) same() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) same_chain() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) same_edge() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) same_ignoring_spaces() (in module pyrosetta.rosetta.utility) same_link() (in module pyrosetta.rosetta.core.io) same_pose() (in module pyrosetta.rosetta.protocols.denovo_design) same_type() (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) same_type_as_me() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) SameSequenceAndDSPositionGrouper (class in pyrosetta.rosetta.protocols.match.output) SameSequenceGrouper (class in pyrosetta.rosetta.protocols.match.output) SameStrand (class in pyrosetta.rosetta.protocols.jumping) sample_all_chi() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sample_all_conformers() (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) sample_all_rotations_at_jump() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) sample_beta() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sample_farnesyl() (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) sample_first() (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) sample_level() (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) sample_loops() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) sample_near_nucleoside_torsion() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) sample_near_suite_torsion() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) sample_ONLY_multiple_virtual_sugar() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sample_pH() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sample_proton_chi() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) sample_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) sample_second() (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) sample_strategy_for_chi() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) sample_third() (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) sample_types() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) sample_zero_probs_at() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) SampleFarnesylMover (class in pyrosetta.rosetta.protocols.farnesyl) sampler_assert_no_virt_sugar_sampling() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sampler_extra_beta_rotamer() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sampler_extra_epsilon_rotamer() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sampler_include_torsion_value_in_tag() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sampler_max_centroid_distance() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sampler_num_pose_kept() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sampler_perform_phosphate_pack() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sampler_silent_file() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sampler_try_sugar_instantiation() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) SamplerPlusPlusType (class in pyrosetta.rosetta.protocols.toolbox) samples() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler method) SampleStrategyData (class in pyrosetta.rosetta.protocols.match.upstream) SampleTiltAngles (class in pyrosetta.rosetta.protocols.membrane.benchmark) sampling_data() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) sampling_data_setup() (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction method) sampling_temperature() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) SandwichFeaturesCreator (class in pyrosetta.rosetta.protocols.features.strand_assembly) SaneMinMover (class in pyrosetta.rosetta.protocols.minimization_packing) SAnode (class in pyrosetta.rosetta.core.scoring.power_diagram) sasa() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) SasaCalc (class in pyrosetta.rosetta.core.scoring.sasa) sasaF2() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) SasaMethod (class in pyrosetta.rosetta.core.scoring.sasa) SasaMethodEnum (class in pyrosetta.rosetta.core.scoring.sasa) SasaMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) SasaRadii (class in pyrosetta.rosetta.core.scoring.sasa) save_all_in_one() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) save_archive() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) save_binary() (pyrosetta.rosetta.protocols.cluster.APCluster method) save_candidates() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) save_checkpoint_file() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) save_cluster_tree() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) save_decoys() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) save_energy() (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) save_fragments() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) save_into_pose() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) save_momento() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) save_schema() (in module pyrosetta.rosetta.protocols.rosetta_scripts) save_status() (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) save_to_file() (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) save_trial_number_to_checkpoint() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) SaveAndRetrieveSidechains (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) saved_accept_file_name() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) saved_reference_pose() (in module pyrosetta.rosetta.protocols.rosetta_scripts) saved_trial_number_file() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) SavePDBInfoMover (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) SavePoseConstraintToFileFilter (class in pyrosetta.rosetta.protocols.constraint_filters) SavePoseMover (class in pyrosetta.rosetta.protocols.rosetta_scripts) saveState() (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) sbisect() (in module pyrosetta.rosetta.numeric.kinematic_closure) sc_min() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) sc_only() (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) scaf_name() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) scalar() (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) scalar_weighted() (in module pyrosetta.rosetta.protocols.constraint_generator) ScalarOption (class in pyrosetta.rosetta.utility.options) ScalarOptionKey (class in pyrosetta.rosetta.utility.options) scale_axis_stagger() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) scale_factor() (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff method) scale_temperatures() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) ScaleMapIntensities (class in pyrosetta.rosetta.protocols.electron_density) scaling() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) SCAN (class in pyrosetta.rosetta.core.pack.task) SCdisplayState (class in pyrosetta.rosetta.protocols.viewer.graphics_states_param) schema() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) score() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.optimization.Particle method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore method) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) score_basis() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) score_basis_125() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) score_by_scoretype() (pyrosetta.rosetta.core.scoring.ScoreFunction method) score_delta() (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) score_diff_after_minimization() (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) score_disulfide() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential method) score_file() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) score_filter() (pyrosetta.rosetta.core.io.silent.SilentFileData method) score_fragment() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) score_fragment_from_cache() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) score_function() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) score_function_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader method) score_map() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) score_one() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) score_only() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) score_pose() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) score_res_z() (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) score_table_filename() (pyrosetta.rosetta.core.io.StructFileRep method) score_table_labels() (pyrosetta.rosetta.core.io.StructFileRep method) score_table_lines() (pyrosetta.rosetta.core.io.StructFileRep method) score_table_weights() (pyrosetta.rosetta.core.io.StructFileRep method) score_threshold() (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) score_type() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) score_type_2_active() (pyrosetta.rosetta.core.scoring.EnergyGraph method) score_type_from_name() (in module pyrosetta.rosetta.core.scoring) score_types() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) score_types_by_method_type() (pyrosetta.rosetta.core.scoring.ScoreFunction method) score_types_for_method() (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator method) score_variation() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) score_variations() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) score_zero_scores() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) scored_base_pair_list() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) scored_frag_close() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) scored_frag_cycle_ratio() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) ScoreEValuator (class in pyrosetta.rosetta.protocols.frag_picker.scores) ScoreEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) scorefile_name() (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) ScoreFileSilentStructCreator (class in pyrosetta.rosetta.core.io.silent) ScoreFunction (class in pyrosetta.rosetta.core.scoring) scorefunction() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) ScoreFunctionFactory (class in pyrosetta.rosetta.core.scoring) ScoreFunctionFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ScoreFunctionInfo (class in pyrosetta.rosetta.core.scoring) ScoreFunctionLoader (class in pyrosetta.rosetta.protocols.parser) scorefxn() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) scorefxn_cen_cst() (pyrosetta.rosetta.protocols.loophash.LocalInserter_SimpleMin method) scorefxn_low() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) scorefxn_minimize() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) scorefxn_pack() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) scorefxn_rama_cst() (pyrosetta.rosetta.protocols.loophash.LocalInserter_SimpleMin method) scorefxn_repack() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) scorefxn_update_from_options() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) ScoreJumpFileSilentStructCreator (class in pyrosetta.rosetta.core.io.silent) scoreline_prefix() (pyrosetta.rosetta.core.io.silent.SilentStruct method) ScoreOnlyJobOutputter (class in pyrosetta.rosetta.protocols.jd2) scores() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) scores_present() (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) ScoreStructText (class in pyrosetta.rosetta.core.io.raw_data) ScoreType (class in pyrosetta.rosetta.core.scoring) ScoreTypeFeaturesCreator (class in pyrosetta.rosetta.protocols.features) scoring() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) scoring_begin() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) scoring_end() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) scoring_grid_loader_ct_namer() (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) ScoringGridLoader (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) SCPA_cyclization_type (class in pyrosetta.rosetta.protocols.cyclic_peptide_predict) scratch_pose() (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepLibrary method) screen_phosphate() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) ScreeningFeaturesCreator (class in pyrosetta.rosetta.protocols.features) SCS_Helper (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_MultiTemplate (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_Result (class in pyrosetta.rosetta.protocols.antibody.grafting) sd() (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) sd_ang() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) sd_dih() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) sd_dis() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) sd_range() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) sdev() (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) sealed_symmetric_fold_tree() (in module pyrosetta.rosetta.core.pose.symmetry) SealFoldTreeMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) search_x() (in module pyrosetta.rosetta.core.scoring.packstat) secant() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) secant_interpolation() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) SecMatchEvaluatorFactory (class in pyrosetta.rosetta.protocols.match.downstream) SecMatchResiduePairEvaluator (class in pyrosetta.rosetta.protocols.match.downstream) secondary_shifts() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) secondary_structure_weights() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) SecondaryIdentity (class in pyrosetta.rosetta.protocols.frag_picker.scores) SecondaryMatcherToDownstreamResidue (class in pyrosetta.rosetta.protocols.match.downstream) SecondaryMatcherToUpstreamResidue (class in pyrosetta.rosetta.protocols.match.downstream) SecondaryMatchUpstreamResProcessor (class in pyrosetta.rosetta.protocols.match.downstream) SecondaryPoseOutputter (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) SecondarySimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) SecondaryStructure (class in pyrosetta.rosetta.core.fragment) SecondaryStructureMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) SecondaryStructureMPM (class in pyrosetta.rosetta.protocols.match) SecondaryStructurePool (class in pyrosetta.rosetta.protocols.frag_picker.quota) SecondaryStructurePotential (class in pyrosetta.rosetta.core.scoring) SecondaryStructureSegmentFeaturesCreator (class in pyrosetta.rosetta.protocols.features) SecondaryStructureType (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) SecondaryStructureWeights (class in pyrosetta.rosetta.core.scoring) secstruct() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.frags.VallData method) SecStructGen (class in pyrosetta.rosetta.core.fragment.picking_old.vall.gen) SecStructMinimizeMultiFunc (class in pyrosetta.rosetta.protocols.ncbb) section() (in module pyrosetta.rosetta.protocols.sparta) section_index() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) see_edge_or_core_or_loop_or_short_edge() (in module pyrosetta.rosetta.protocols.features.strand_assembly) see_whether_model_is_H_bonded_by_terminal_strands() (in module pyrosetta.rosetta.protocols.legacy_sewing) see_whether_sheet_is_antiparallel() (in module pyrosetta.rosetta.protocols.features.strand_assembly) see_whether_sheets_can_be_combined() (in module pyrosetta.rosetta.protocols.features.strand_assembly) see_whether_this_sw_has_SS_bond() (in module pyrosetta.rosetta.protocols.features.strand_assembly) seed() (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) seek_beg() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) seekp() (pyrosetta.logging_support.PythonLoggingSink method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.TracerImpl method) Segment (class in pyrosetta.rosetta.protocols.denovo_design.components) segment() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) segment1_ids() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) segment2_ids() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) segment_id() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) segment_ids() (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) segment_length() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) segment_to_local() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) segment_to_pose() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) SegmentedAtomPairConstraintGenerator (class in pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator) SegmentGraph (class in pyrosetta.rosetta.protocols.legacy_sewing) segmentID() (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.pose.PDBInfo method) SegmentInsert (class in pyrosetta.rosetta.protocols.forge.build) SegmentRebuild (class in pyrosetta.rosetta.protocols.forge.build) segments() (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) SegmentSwap (class in pyrosetta.rosetta.protocols.forge.build) select() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) select_best_poses() (in module pyrosetta.rosetta.protocols.ligand_docking) select_cav_balls() (in module pyrosetta.rosetta.core.scoring.packstat) select_epitope_residues() (in module pyrosetta.rosetta.protocols.antibody) select_final_loop() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) select_fragments() (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector method) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector method) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector method) select_interface_residues() (in module pyrosetta.rosetta.protocols.interface) select_loop_frags() (in module pyrosetta.rosetta.protocols.loops) select_loop_residues() (in module pyrosetta.rosetta.protocols.loops) select_only_alpha_aas() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) select_only_FAMILYVW() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) select_orient_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) select_points() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) select_poses() (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) select_positive_phi() (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) select_random() (pyrosetta.rosetta.protocols.jumping.JumpSelector method) select_RBsegments() (in module pyrosetta.rosetta.protocols.rbsegment_relax) select_score() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) selected() (pyrosetta.rosetta.protocols.moves.SwitchMover method) SelectedResidueCountMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) SelectedResiduesMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) SelectedResiduesPyMOLMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) selection_is_symmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) selection_positions() (in module pyrosetta.rosetta.core.select.residue_selector) selector() (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) Selector_AA (class in pyrosetta.rosetta.core.chemical) Selector_CMDFLAG (class in pyrosetta.rosetta.core.chemical) Selector_HAS_ATOMS (class in pyrosetta.rosetta.core.chemical) Selector_MATCH_VARIANTS (class in pyrosetta.rosetta.core.chemical) Selector_NAME1 (class in pyrosetta.rosetta.core.chemical) Selector_NAME3 (class in pyrosetta.rosetta.core.chemical) Selector_NO_VARIANTS (class in pyrosetta.rosetta.core.chemical) Selector_PROPERTY (class in pyrosetta.rosetta.core.chemical) selector_type (class in pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector) Selector_UPPER_POSITION (class in pyrosetta.rosetta.core.chemical) Selector_VARIANT_TYPE (class in pyrosetta.rosetta.core.chemical) SelectorLogicParser (class in pyrosetta.rosetta.core.select.residue_selector) SelectResiduesWithinChainOperation (class in pyrosetta.rosetta.protocols.task_operations) send_char_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) send_data_to_head_node() (in module pyrosetta.rosetta.basic.mpi) send_double_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) send_doubles_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) send_integer_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) send_integers_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) send_size_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) send_sizes_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) send_string_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) sendMessage() (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) seq1() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) seq2() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) seq_design_strategy_to_enum() (in module pyrosetta.rosetta.protocols.antibody.design) seq_design_strategy_to_string() (in module pyrosetta.rosetta.protocols.antibody.design) SeqDesignStrategyEnum (class in pyrosetta.rosetta.protocols.antibody.design) seqmap() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) seqpos() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) seqpos_for_geomcst() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) seqposes_no_mutate_str() (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) seqprof() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) seqprof_wt_aa() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) seqs_from_cmd_lines() (in module pyrosetta.rosetta.core.sequence) sequence() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) sequence_comment_id() (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) sequence_constraint() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) sequence_map_from_pdbinfo() (in module pyrosetta.rosetta.core.pose) sequence_mapping() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) sequence_matches() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) sequence_mutated() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) sequence_space() (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) SequenceAlignmentHasher (class in pyrosetta.rosetta.core.sequence) SequenceCoupling1BDConstraintCreator (class in pyrosetta.rosetta.protocols.constraints_additional) SequenceCouplingConstraintCreator (class in pyrosetta.rosetta.protocols.constraints_additional) SequenceCreator (class in pyrosetta.rosetta.core.sequence) SequenceDistance (class in pyrosetta.rosetta.protocols.simple_filters) SequenceIdentity (class in pyrosetta.rosetta.protocols.frag_picker.scores) SequenceMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) SequenceMotifTaskOperation (class in pyrosetta.rosetta.protocols.task_operations) SequenceMover (class in pyrosetta.rosetta.protocols.moves) SequenceProfileConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) SequenceShiftMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) sequential_order() (pyrosetta.rosetta.protocols.loops.Loops method) serialize() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) serialize_graph_json() (in module pyrosetta.rosetta.protocols.legacy_sewing) serialize_ids() (in module pyrosetta.rosetta.protocols.features) serialize_residue_xyz_coords() (in module pyrosetta.rosetta.protocols.features) serialize_weights() (pyrosetta.rosetta.core.scoring.ScoreFunction method) SerializedLoop (class in pyrosetta.rosetta.protocols.loops) Set() (in module pyrosetta) set() (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) Set_AA (class in pyrosetta.rosetta.core.chemical) set_aa() (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) set_aa_composition_setup_files() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_aa_probabilities() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_aa_probabilities_from_file() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_aa_probability_set() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_ab_fold_tree() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) set_ab_info() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) set_abba_bins_binfile_contents() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_abego() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) set_abort_on_failed_loop() (pyrosetta.rosetta.protocols.LoopRebuild method) set_absolute_stereochemistry() (pyrosetta.rosetta.core.chemical.Atom method) set_absolute_threshold() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) set_abstract() (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) set_accept_aborted_loops_() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) set_accept_blocks_missing_header() (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) set_acceptor_selector() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) set_accessed() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) set_active_restype_index() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) set_active_site_grid() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) set_add_alanine_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) set_add_c_terminal_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) set_add_constraints() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_add_hydrophobic_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) set_add_lead_zero_to_tag() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_add_ligand_to_pose() (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) set_add_n_terminal_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) set_add_overall_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) set_add_peptide_plane_variants() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_add_target_to_pose() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) set_add_target_types() (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) set_add_to_current() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_add_virt_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_add_virt_res_as_root() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_additional_task_operarations() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_additional_type_to_add() (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) set_additional_type_to_remove() (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) set_adduct_flag() (pyrosetta.rosetta.core.chemical.ResidueType method) set_aggregate_function() (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) set_akash_dyepos() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_align_file() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_align_only_over_base_atoms() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_align_to_native() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) set_alignment_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_all_chi() (pyrosetta.rosetta.core.conformation.Residue method) set_all_current_jobs_as_deletable() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) set_all_extra_parameters() (pyrosetta.rosetta.core.chemical.AtomType method) set_all_nu() (pyrosetta.rosetta.core.conformation.Residue method) set_all_ring_nu() (pyrosetta.rosetta.core.conformation.Residue method) set_allow_anchor_repack() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_allow_base_pair_only_centroid_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_allow_bondangles() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_allow_bondlengths() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_allow_bulge_at_chainbreak() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_allow_chain_boundary_jump_partner_right_at_fixed_BP() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_allow_design_cdr() (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) set_allow_design_neighbor_antigen() (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) set_allow_design_neighbor_framework() (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) set_allow_dihedrals() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_allow_fixed_res_at_moving_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_allow_rebuild_bulge_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_allow_syn_pyrimidine() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_allow_virtual_o2prime_hydrogens() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) set_allow_virtual_side_chains() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) set_allowed_failure_before_extend() (pyrosetta.rosetta.protocols.LoopRebuild method) set_allowed_failure_before_stop() (pyrosetta.rosetta.protocols.LoopRebuild method) set_allowed_residues_by_position() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_alpha() (pyrosetta.rosetta.core.pose.Pose method) set_already_completed_job_count() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_alternative_search_paths() (pyrosetta.rosetta.utility.io.izstream method) set_always_rotamer_one() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) set_ambiguous_hnq() (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) set_anchor_noise_constraints_mode() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_anchor_via_constraints() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_ang_D1D2D3() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_ang_U1D2_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_ang_U2D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_angle() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) set_angle1_func() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_angle2_func() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_angle_atom() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) set_angle_exponent() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_angle_length_relax_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_angle_max() (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) set_angle_range() (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) set_angle_ranges() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) set_angle_relax_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_angle_sd() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_angle_shift_factor() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_angle_threshold() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) set_angles() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) set_antibody_info() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) set_antiparallel_weight() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_apply_vdw_cut() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_apply_virtual_res_variant_at_dinucleotide() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) set_architect() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) set_archive() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) set_assert_jump_point_in_fixed_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_asymm_unit_fold_tree() (in module pyrosetta.rosetta.core.conformation.symmetry) (in module pyrosetta.rosetta.core.pose.symmetry) set_atmid() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) set_atom_base() (pyrosetta.rosetta.core.chemical.ResidueType method) set_atom_level_domain_map() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_atom_mode() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) set_atom_names_for_distance_measure() (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) set_atom_pair_func() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_atom_pair_sd() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_atom_type() (pyrosetta.rosetta.core.chemical.ResidueType method) set_atom_type_set() (pyrosetta.rosetta.core.chemical.ResidueType method) set_atoms1() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_atoms2() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_atoms_per_residue() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_atr_rep_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_atr_rep_screen_for_docking() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_attach_boinc_ghost_observer() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) set_attached_res() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) set_attachment_type() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) set_attachments() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) set_auto_detect_glycan_connections() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_auto_detect_symmetry() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) set_auto_tune() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_auto_update() (pyrosetta.rosetta.core.scoring.NeighborList method) set_autofoldtree() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) set_autotemp() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) set_babmotifs() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) set_backbone() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_backbone_backbone_acceptor() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) set_backbone_backbone_donor() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) set_backbone_burial() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) set_backbone_exposed() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) set_backbone_heavyatom() (pyrosetta.rosetta.core.chemical.ResidueType method) set_backbone_only() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) set_bad() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) set_bad_nter() (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) set_ball_radius() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_base_atom_name() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_base_base_atom_name() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_base_partner() (in module pyrosetta.rosetta.core.scoring.dna) set_base_segment_chainbreak_constraints() (in module pyrosetta.rosetta.protocols.dna) set_base_type_cop() (pyrosetta.rosetta.core.chemical.ResidueType method) set_bb() (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) set_bb_bb() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_bb_grid() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) set_bb_movemap() (in module pyrosetta.rosetta.protocols.hydrate) set_bb_torsion() (in module pyrosetta.rosetta.core.pose) set_bb_true_range() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_behaviour() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_being_set() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_beta() (pyrosetta.rosetta.core.pose.Pose method) set_bfactors_from_atom_id_map() (in module pyrosetta.rosetta.core.pose) set_bias_sampling() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_bIdealLoopClosing() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) set_bin() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) set_bin_name() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) set_bin_params_file_name() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) set_binfile_and_load() (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) set_bInitDofs() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) set_binname() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) set_blueprint() (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) set_boltz_rank() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_boltzmann_temp() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) set_bond_angle() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) set_bond_length() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) set_boolean_option() (in module pyrosetta.rosetta.basic.options) set_boolean_vector_option() (in module pyrosetta.rosetta.basic.options) set_bounded() (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_bounded_width() (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) set_bounding_box() (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) set_bps_moves() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_branch_atom() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) set_branches() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_branches_true_range() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_bridge() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) set_bridge_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_broker() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) set_buffer_length() (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) set_build_all_loops_() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) set_build_attempts_() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) set_build_overlap() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) set_build_round1_hits_twice() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) set_bulge_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) set_bulges() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) set_bump_check() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_bump_overlap_factor() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_bump_tolerance() (pyrosetta.rosetta.protocols.match.Matcher method) set_bundle_symmetry() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) set_bundle_symmetry_copies() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) set_burial_cutoff() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_c_cyd_seqpos() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_ca_only() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) set_cache_selection() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_cache_size() (in module pyrosetta.rosetta.basic.database) set_cacheable_cluster_data_to_pose() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) set_cached_resfile() (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) set_calc_dSASA() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_calc_hbond_sasaE() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_calc_in_hours() (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) set_calc_rms_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_calculate_jacobians() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) set_calculate_silent_Es() (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) set_calculated() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) set_calculation_method() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_calculator_by_name() (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) set_camelid() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) set_can_be_deleted() (pyrosetta.rosetta.protocols.jd2.Job method) set_candidates_collector() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_cart_min() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_cartesian() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) set_cartesian_bonded_linear() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_cartesian_bonded_parameters() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_cartesian_relax_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_catalytic_atoms() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) set_ccd_close() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_ccd_close_res() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) set_CCD_torsions_to_zero() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) set_cdr() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) set_CDR_cluster() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) set_cdr_design_options() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) set_cdr_only() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) set_cdr_range() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) set_cdr_set_options() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_cdrs() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) set_cen_scorefunction() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_cen_scorefxn() (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) set_center() (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) set_center_jumps_in_single_stranded() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_centroid() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) set_centroid_loop_building() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) set_centroid_output() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_centroid_score_diff_cut() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_centroid_scorefunction() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_centroid_scorefxn() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_centroid_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_centroid_weights() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_chainbreak_max() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) set_chainbreak_weight() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_chains() (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) set_chains_whose_residues_are_separate_chemical_entities() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_change_chi_without_replacing_residue() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) set_changed() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) set_check_if_residues_are_Ctermini() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_check_if_residues_are_Ntermini() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_check_ss() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) set_chemical_bond_from_upstream_to_downstream() (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_chi() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) set_chi_according_to_coordinates() (in module pyrosetta.rosetta.core.conformation) set_chi_true_range() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_choices() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) set_choose_random() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) set_cis_peptide_bonds() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) set_cl_value() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) set_cluster() (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) set_cluster_by_all_atom_rmsd() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_cluster_csts_data_cutoff() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_cluster_csts_use_mean_cst_data() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_cluster_csts_use_outlier_data() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_cluster_data() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) set_cluster_radius() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_cluster_rmsd() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_clusters() (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) set_combine_long_loop_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_command() (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation method) set_comp_constraint_aa() (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) set_comparer_info() (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) set_comparison_pose() (pyrosetta.rosetta.protocols.analysis.simple_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.TotalEnergyMetric method) set_comparison_type() (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_completed() (pyrosetta.rosetta.protocols.jd2.Job method) set_composite_action() (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_compute_interface_delta_hbond_unsat() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_compute_interface_energy() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_compute_interface_sc() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_compute_packstat() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) set_compute_separated_sasa() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_computed() (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) set_cone_parameters() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) set_conformer_sampling_sd() (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) set_connect_info_cutoff() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_cons_design_data_source() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_conserved() (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) set_consider_mainchain_only() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) set_const_data() (pyrosetta.rosetta.core.pose.Pose method) set_constrain_to_closest() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_constraint_func() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) set_constraint_weight() (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_constraints() (in module pyrosetta.rosetta.protocols.rbsegment_relax) set_constraints_from_link_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_constraints_only() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_contact_resnum_string() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_contact_resnums_string() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_contact_selector() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_coord_frame_ref() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) set_coordinate_cacher() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) set_coordinate_constraints_during_minimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_coordinates() (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) set_copy_DOF() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) set_copy_identity() (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) set_copy_torsions() (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) set_corresponding_atoms_robust() (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) set_cos_theta() (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) set_count_gly_as_polar() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) set_crystinfo() (pyrosetta.rosetta.core.pose.PDBInfo method) set_cst_action() (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) set_cst_block() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) set_cst_file() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_cst_term_ramping() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_cst_weight() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_cstAtoms() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) set_cstfile() (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) set_cstio() (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) set_cstweight() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) set_current_confnum() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) set_current_job() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) set_current_tag() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) set_custom_angle() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_custom_dihedral() (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) set_custom_rama_table() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) set_cut() (pyrosetta.rosetta.protocols.loops.Loop method) set_cutoff() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_cutoff_buried_surface_area() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) set_cutoff_distance() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) set_cutoffs() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_cutpoint() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_cutpoint_closed_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_cycles_inner() (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) set_cycles_outer() (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) set_cyclization_type() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_d() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) set_D_alpha_compfile_contents() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_D_beta_compfile_contents() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_data_source() (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) set_database_name() (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) set_database_pq_schema() (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) set_db_path() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) set_db_reporter() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) set_dcut() (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) set_dcut1() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) set_dcut2() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) set_ddG_cutoff() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) set_debug() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) set_decoy_compatibility() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) set_decoy_tag() (pyrosetta.rosetta.core.io.silent.SilentStruct method) set_decoys_returned() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) set_deep_optimization() (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) set_default() (pyrosetta.rosetta.core.scoring.FACTSPotential method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_default_coordinate_settings() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_default_final_stream() (pyrosetta.rosetta.basic.TracerImpl method) set_default_mc() (pyrosetta.rosetta.protocols.LoopRebuild method) set_default_minimization_settings() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_default_minimizer() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_default_movemap() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_default_moveset_phase1() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_default_moveset_phase2() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_default_moveset_phase3() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_default_options() (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) set_default_scores() (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) set_default_settings() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) set_default_value() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_defaults() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_degree_vicinity() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) set_degrees() (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) set_delta() (pyrosetta.rosetta.core.pose.Pose method) set_delta_omega0() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_delta_omega1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_delta_omega1_all() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_delta_t() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_delta_z1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_density_sc_scale_byres() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_deriv_check_result() (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) set_deriv_cutoff() (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) set_design() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) set_design_framework_conservative() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) set_design_framework_conserved_res() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) set_design_H3_stem() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) set_design_loop() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) set_design_neighbors() (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) set_design_options() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_design_protocol() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_design_target_res() (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) set_design_taskset() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_design_x_positions() (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) set_designing_with_noncanonicals() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) set_desymmeterize() (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler method) set_detect_bonds() (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) set_detect_pseudobonds() (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) set_dew_waters_not_to_be_included() (in module pyrosetta.rosetta.protocols.hydrate) set_dG_weight() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) set_dihedral() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) set_dihedral_constraint_weight() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_dihedral_mask() (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) set_dihedrals_from_linkage_conformer_data() (in module pyrosetta.rosetta.core.pose.carbohydrates) set_dimension() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) set_dis() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_dis_D1D2() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_dis_D2D3() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_dis_U1D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_disable_packing_and_design() (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) set_disable_sampling_of_loop_takeoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_disabled_except_during_packing() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) set_disallow_deletion_of_last_residue() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) set_disallow_pack_polar_hydrogens() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_disallow_realign() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_dist_cutoff_multiplier() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) set_dist_exponent() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_distance() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) set_distinguish_pucker() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_disulfide_atom_name() (pyrosetta.rosetta.core.chemical.ResidueType method) set_disulfide_file() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_do_add_delete() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) set_do_inner() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_do_not_autoassign_SS() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_do_not_sample_multiple_virtual_sugar() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_do_outer() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_do_sfxn_eval_every_iteration() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_dock_each_chunk() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_dock_each_chunk_per_chain() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_dock_high_res_scorefunction() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) set_dock_low_res_scorefunction() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) set_dock_mcm_protocol() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) set_dock_min() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_dock_min_protocol() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) set_dock_pert() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_dock_post_graft() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_dock_ppk() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_dock_ppk_protocol() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) set_dock_rounds() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_dock_rtmin() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_docking_highres_mover() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_docking_local_refine() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_dof() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pose.Pose method) set_DOF() (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) set_domain() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) set_donor_selector() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) set_donor_structure() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_downstream_algorithm() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) set_downstream_builder() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_downstream_master() (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) set_downstream_pose() (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_downstream_restype() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) set_drift() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_dry_run() (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) set_dSASA_cutoff() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) set_dsbuilder() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) set_dump() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_dump_pdb() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_dump_silent() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_dumping_app() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_edge_data() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) set_edge_weight() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_effective_sequence_separation() (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) set_efficiency() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) set_elec_sigmoidal_die_params() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_else() (pyrosetta.rosetta.protocols.filters.IfThenFilter method) set_end() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) set_end_bias() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) set_energy() (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) set_energy_cutoff() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_energy_landscape_evaluator() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) set_energy_method_options() (pyrosetta.rosetta.core.scoring.ScoreFunction method) set_ensemble1() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_ensemble2() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_ensured_sites() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) set_entity_element() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) set_entity_template() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) set_enumerate() (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) set_enumeration_shell() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) set_enzio_param() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) set_enzyme() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) set_epitope_residues() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_epsilon() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_equiv() (pyrosetta.rosetta.protocols.symmetry.NCSResMapping method) set_error_on_out_of_bounds_index() (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) set_errorfull_deltaE_threshold() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_etable() (pyrosetta.rosetta.core.scoring.ScoreFunction method) set_euler_bin_widths() (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) set_evaluate_local() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) set_evaluation() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) set_evaluators() (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) set_exclude_chain_termini() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) set_exclude_polar_atoms_by_charge() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_excluded_sites() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) set_exit_if_missing_heavy_atoms() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_expand_loop_takeoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_explicit_hydrogen_included_radii_set() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_expression() (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) set_extend_h3() (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) set_extend_ss() (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator method) set_extended() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.Loops method) set_extended_loop() (pyrosetta.rosetta.protocols.LoopRebuild method) set_extended_torsions() (in module pyrosetta.rosetta.protocols.loops) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) set_extended_torsions_and_idealize_loops() (in module pyrosetta.rosetta.protocols.loops) set_external_position() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) set_external_position_for_resA() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) set_external_position_for_resB() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) set_extra_chi() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_extra_data_1() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) set_extra_data_2() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) set_extra_data_3() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) set_extra_minimize_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_extra_parameter() (pyrosetta.rosetta.core.chemical.AtomType method) set_extra_penalty() (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) set_extra_samples() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) set_fa_dun_cutoff() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) set_fa_dun_cutoff_for_constraint() (pyrosetta.rosetta.protocols.match.Matcher method) set_fa_score_function() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) set_fa_scorefunction() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_fa_scorefxn() (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) set_fallback_strategy() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_farray_from_sso() (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) set_favor_native_bonus() (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) set_fcen10() (pyrosetta.rosetta.core.scoring.CenListInfo method) set_fcen12() (pyrosetta.rosetta.core.scoring.CenListInfo method) set_fcen6() (pyrosetta.rosetta.core.scoring.CenListInfo method) set_file_contents() (pyrosetta.rosetta.utility.io.FileContentsMap method) set_file_option() (in module pyrosetta.rosetta.basic.options) set_file_reading_token() (pyrosetta.rosetta.protocols.loops.Loops method) set_file_vector_option() (in module pyrosetta.rosetta.basic.options) set_filename() (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) set_filter() (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) set_filter_behaviour() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_filter_by_lj() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_filter_by_phipsi() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_filter_during_design() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_filter_native_big_bins() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_filter_out_high() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) set_filter_out_low() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) set_filter_structs() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) set_filter_type() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) set_filter_user_alignment_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_filter_virtual_res_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_filters() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_final_frlx_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_final_min_pack_min() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) set_finer_sampling_at_chain_closure() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_finish_scorefxn() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) set_finite() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) set_first_expression() (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) set_fitness() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) set_fix_angles() (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_fix_backbone() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_fix_catalytic_aa() (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) set_fix_lengths() (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_fix_torsions() (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_fixed_energies() (pyrosetta.rosetta.core.scoring.MinimizationGraph method) set_fixed_if_moving() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) set_fixed_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_fixed_residues() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_flank_size() (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) set_floating_base() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_floating_base_anchor_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_focus() (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) set_focus_selector() (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) set_focused_geomcst_id() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) set_fold_tree_from_symm_data() (in module pyrosetta.rosetta.core.conformation.symmetry) set_fold_tree_io() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_fold_tree_root() (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) set_folder() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) set_folding_window() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) set_foldtree() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) set_force_align() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_force_anti_chi_res_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_force_bitflip() (pyrosetta.rosetta.core.io.silent.SilentStruct method) set_force_centroid_interaction() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_force_cluster() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_force_internal() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_force_job_purging() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) set_force_north_paper_db() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_force_north_sugar_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_force_phosphate_instantiation() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) set_force_repack() (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) set_force_south_sugar_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_force_syn_chi_res_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_force_user_defined_jumps() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_forced_silent_struct_type() (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) set_fraction() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) set_fractions() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) set_frag3() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_frag_files() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_frag_size() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) set_frag_sizes() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_fragments() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) set_frags() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_free_peptide() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) set_free_rsd() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_from_cdr() (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) set_from_other_chains() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_from_same_chain() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_from_scheme() (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) set_ft_mover() (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) set_full_length_loop_rmsd_clustering() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) set_full_model_parameters() (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) set_full_repack() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_full_to_sub() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) set_fullatom() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_fullatom_loop_building() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) set_fullatom_scorefunction() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_fullatom_scorefxn() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) set_function() (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) set_Fv() (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) set_gamma() (pyrosetta.rosetta.core.pose.Pose method) set_gasteiger_atom_type() (pyrosetta.rosetta.core.chemical.ResidueType method) set_gasteiger_typeset() (pyrosetta.rosetta.core.chemical.ResidueType method) set_gaussian() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) set_gaussian_stdevs_recces_turner() (in module pyrosetta.rosetta.protocols.recces) set_gaussian_stdevs_thermal_sampler() (in module pyrosetta.rosetta.protocols.recces) set_general_phi_sd() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_general_psi_sd() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_generous_hbonds_() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_geomcst_for_superposition_from_enz_io() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) set_ghost_loops() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_global() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) set_global_optimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_global_sample_res_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_glycam_pdb_format() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_glycan_iupac_bb_torsions() (in module pyrosetta.rosetta.core.pose.carbohydrates) set_glycan_iupac_chi_torsions() (in module pyrosetta.rosetta.core.pose.carbohydrates) set_glycan_relax_rounds() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) set_glycan_sequon_type() (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) set_GlyCorrection_values_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_glycosidic_torsion() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) set_glycosylation() (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) set_glycosylation_position() (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) set_glycosylation_weights() (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) set_glycosylations() (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) set_graft_design_cdrs() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_graft_design_options() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_grow_attempts_() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) set_guarantee_no_DNA() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_guarded_loops_not_in_charge() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) set_handedness_score_flag() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_hardsphere_bump_check() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_has_silent_in() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) set_hash_euclidean_bin_width() (pyrosetta.rosetta.protocols.match.Matcher method) set_hash_euclidean_bin_widths() (pyrosetta.rosetta.protocols.match.Matcher method) set_hash_euler_bin_width() (pyrosetta.rosetta.protocols.match.Matcher method) set_hash_euler_bin_widths() (pyrosetta.rosetta.protocols.match.Matcher method) set_hb_e_cutoff() (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) set_hbnet_energy_ramping() (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) set_hbond_energy_cutoff() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) set_hbond_options() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) set_hbonds() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) set_heat_after_cycles() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) set_helix() (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) set_helix_index() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_helix_to_copy() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_highres_score_func() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) set_highres_scorefxn() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_hit_cacher() (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) set_hydrate_magnesiums() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_icoor() (pyrosetta.rosetta.core.chemical.ResidueType method) set_id() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) set_ideal_abego() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) set_ideal_angle_about_contact() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ideal_angle_about_metal() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ideal_dihedral_3() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ideal_dihedral_about_contact() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ideal_dihedral_about_metal() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ideal_distance() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ideal_xyz() (pyrosetta.rosetta.core.chemical.ResidueType method) set_idealize() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) set_idealize_h3_stems() (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) set_idealize_insert() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_idealize_loop_first() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_idealize_torsions() (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) set_IGEdgeReweights() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) set_ignore_bb_heavy_unsats() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_ignore_default_docking_task() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_ignore_default_task() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) set_ignore_FARFAR_no_auto_bulge_parent_tag() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_ignore_FARFAR_no_auto_bulge_tag() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_ignore_light_chain() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_ignore_pose_datacache() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_ignore_pose_profile_length_mismatch() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) set_ignore_segments() (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) set_ignore_sugars() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_ignore_surface_res() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_ignore_unconnected_upper() (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) set_ignore_unmatched_virtual_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_ignore_unrecognized_res() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_ignore_waters() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_ignore_zero_occupancy() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_implicit_hydrogen_included_radii_set() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_include_carbon_sulfer_only_in_hydrophobic_calc() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_include_cdr4_in_optimization() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_include_default_linear_chainbreak() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) set_include_focus_in_subset() (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) set_include_hydrogens_explicitly() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_include_native_restype() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_include_native_type() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_include_neighbors() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) set_include_probe_radius_in_atom_radii() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_include_probe_radius_in_calc() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) set_include_protein_omega() (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) set_include_root() (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) set_indent() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) set_index() (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) set_inherit_scorefxn_temperature() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) set_inner_ca_only() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_inner_cycles() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_inner_min_seq_sep() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_inner_sd() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_inner_unweighted_function() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_inner_use_harmonic_function() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_inner_weight() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_input_pose() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) set_input_set() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) set_input_set_selector() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) set_input_tags() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_insert_flexibility() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_insert_region() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) set_instruction_file() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_instruction_file_path() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) set_integer_option() (in module pyrosetta.rosetta.basic.options) set_integer_vector_option() (in module pyrosetta.rosetta.basic.options) set_integration_test_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_intensity() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) set_interface() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) set_interface_chains() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) set_interface_definition_task_operation() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_interface_dis() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_interface_distance() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) set_interface_jump() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_intermediate_structs() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) set_internal_cycles() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) set_interval() (pyrosetta.rosetta.protocols.checkpoint.Timer method) set_invert() (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) set_invert_helix() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_invert_task() (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) set_invrots_for_listnum() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) set_ios_hook() (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerImpl method) set_is_do_minimize() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_is_dump_cyclic_poses() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_is_dump_peptide_pose() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_is_dump_prepared_pose() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_is_dump_report_file() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_is_report_gzip() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_is_skip_zero_isc() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_iterations() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) set_iterations_per_phase() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) set_job_inputter() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) set_job_outputter() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) set_jobindex_on_originating_node() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) set_jump() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) set_jump_atom_stub_id() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) set_jump_atoms() (pyrosetta.rosetta.core.kinematics.FoldTree method) set_jump_now() (pyrosetta.rosetta.core.kinematics.AtomTree method) set_jump_num() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_jump_point_pair_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_jump_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_jump_sample() (pyrosetta.rosetta.protocols.jumping.JumpSetup method) set_jump_selector() (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) set_jumpAtoms() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) set_just_polar_hydrogens() (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_just_rna_backbone() (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_keep_covalent() (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) set_keep_filters() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_keep_input_foldtree() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) set_keep_input_protonation_state() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_keep_pdb_info_labels() (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) set_keep_pose_in_memory() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_keep_task_allowed_aas() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_keep_top_designs() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_keep_unknown_aas() (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) set_keep_virtual_residues() (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) set_kic_modeler_if_relevant() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_kic_sampling() (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) set_kinematics() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) set_kinmover() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) set_kt() (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) set_kT() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) set_L_alpha_compfile_contents() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_L_beta_compfile_contents() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_label() (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) set_landing_domain() (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) set_landing_pos() (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) set_last_accepted() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) set_last_accepted_pose() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) set_last_score() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) set_layer() (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) set_layer_as_greater_than_or_equal_to() (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) set_layer_as_less_than_or_equal_to() (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) set_layer_mode() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_layer_size() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) set_layers() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_length() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) set_lengths() (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) set_ligand_atom_name() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ligand_jump_id() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_ligand_resnum() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_ligand_resnum_string() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ligand_selector() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ligand_weight() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_ligpose_rotamer() (in module pyrosetta.rosetta.protocols.match) set_limit() (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) set_limit_only_to_length() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) set_linecount_offset() (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader method) set_linker_name() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_live() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) set_lj_atr_weight() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_lj_cutoff() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_lj_ramp_cycles() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_lj_ramp_inner_cycles() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_lj_rep_weight() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_lj_sol_weight() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_local_movemap() (in module pyrosetta.rosetta.protocols.vip) set_local_refine() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_local_rotamer_id() (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) set_localstrandpair_penalty() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_location_in_parent_node() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) set_logging_sink() (in module pyrosetta.logging_support) set_long_range_container() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) set_loop() (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) set_loop_ang() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_loop_begin_and_end() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_loop_cluster_radius() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_loop_combine_rate_() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) set_loop_cutpoint_in_pose_fold_tree() (in module pyrosetta.rosetta.protocols.loops) set_loop_dih() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_loop_file_name_and_reset() (pyrosetta.rosetta.protocols.loops.Loops method) set_loop_pose() (in module pyrosetta.rosetta.protocols.generalized_kinematic_closure) set_loopres_base2_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_loopres_base_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_loops() (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) set_loops_and_anchor() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_loops_from_file() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) set_loops_pointer() (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) set_lores() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_low_energy_ring_conformers() (pyrosetta.rosetta.core.chemical.ResidueType method) set_low_res_protocol_only() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_lower_connect_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) set_lower_residues() (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) set_lower_segment() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_lower_threshold() (pyrosetta.rosetta.protocols.filters.IfThenFilter method) set_lower_value() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_lowest() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) set_lowest_energy_ring_conformer() (pyrosetta.rosetta.core.chemical.ResidueType method) set_lowest_score_pose() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) set_lowres_score_func() (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) set_lowres_scorefxn() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_lt_dih() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_magnitude() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) set_mainchain_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) set_maintain_links() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_manager() (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) set_mapfile_activated() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_match_string() (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_max_accepted_trials() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_max_allowed_oversaturated() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) set_max_angle_disp_4() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_max_angle_disp_7() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_max_angle_disp_slope() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_max_atoms() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_max_attempts() (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) set_max_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_max_bond_length() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_max_decoys() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_max_distance() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) set_max_dslf_energy() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_max_dslf_pot() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_max_nstruct() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_max_radius() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_max_repeats() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_max_rms() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_max_sample_iterations() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) set_max_strand_dist_cutoff() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_max_struct() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_max_struct_per_radius() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_max_trial_num() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) set_max_tries_multiplier_for_ccd() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_maxfrac() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) set_maxtrials() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_mc() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_mcfi() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) set_membrane() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_membrane_info() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) set_membrane_jump() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) set_memory_max_for_rpes() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_merge_behavior_manager() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) set_metal_bond_angle_constraint_multiplier() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_metal_bond_dist_constraint_multiplier() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_metal_bond_LJ_multiplier() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_metal_resnums_string() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_metal_selector() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_metals_angle_constraint_multiplier() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_metals_detection_LJ_multiplier() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_metals_distance_constraint_multiplier() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_method_weights() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) set_metropolis_hastings_mover() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) set_mg_calculation_annotated_sequence() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) set_min_allowed_score() (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) set_min_atoms() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_min_bb() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) set_min_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_min_bond_length() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_min_chi() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) set_min_distance() (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) set_min_frag_length() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) set_min_helix_length() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) set_min_num_south_sugar_filter() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_min_options() (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) set_min_overlap() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) set_min_rings() (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) set_min_rms() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_min_seq_sep() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) set_min_tol() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) set_min_tolerance() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_min_type() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_minfrac() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) set_minimization_graph() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) set_minimize_after_delete() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) set_minimize_all() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) set_minimize_and_score_native_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_minimize_and_score_sugar() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_minimize_single_res() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) set_minimize_waters() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_minimizer_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_minimizer_rename_tag() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_minmover() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) set_mintype() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_mirror_symm() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) set_mirrored_relative_to_type() (pyrosetta.rosetta.core.conformation.Residue method) set_missing_dens_as_jump() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_mm() (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) set_mm_atom_type() (pyrosetta.rosetta.core.chemical.ResidueType method) set_mode() (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) set_model_and_remove_capping_residues() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) set_model_group() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) set_model_with_density() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_modes() (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) set_moltenres() (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) set_monte_carlo() (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) set_motif() (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation method) set_motifs() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) set_movable_group() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_movable_jumps() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) set_move_element() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) set_move_jumps_between_chains() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_move_map() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) set_move_map_for_centroid_loop() (in module pyrosetta.rosetta.protocols.loops) set_move_takeoff_torsions() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) set_move_type() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) set_moveable_jumps() (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) set_movemap() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) set_movemap_factory() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_movemaps() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_movement() (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) set_mover() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) set_mover_cycles() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_mover_tag() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) set_mover_weight() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) set_moves() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) set_moving_residues() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_mpi_rank() (pyrosetta.rosetta.utility.SimulateMPI method) set_mu() (pyrosetta.rosetta.core.pose.Pose method) set_multi_template_regions() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) set_multifunc() (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) set_must_switch_bins() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) set_mut_pose() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) set_mutate_to_glycine() (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) set_mutation_rate() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) set_my_rank() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_n_candidates() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_n_cycle() (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_n_cycles() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_n_cyd_seqpos() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_n_frags() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_n_geometric_constraints() (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) set_n_helices() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) set_n_partners() (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) set_n_sample() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_n_samples_per_side_of_nrchi_bin() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_n_samples_wi_sd_range() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_name() (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) set_name1() (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) set_natbias_helices_sheet_pot() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) set_natbias_hpairpot() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) set_natbias_spairpot() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) set_native() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_native_alignment_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_native_cdr_sequence() (in module pyrosetta.rosetta.protocols.antibody.design) set_native_distance_viol() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) set_native_edensity_score_cutoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_native_in_mover() (in module pyrosetta.rosetta.protocols.jd2) set_native_pose() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) set_native_sequence() (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) set_native_spairset() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential method) set_native_virtual_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) set_nblist() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) set_nbrs() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) set_ncluster() (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) set_ncycle() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) set_ncycles() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_neighbor_dis() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_neighbor_distance() (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) set_neighborhood_parameters() (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) set_netcharge_setup_files() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_network_anchoring() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) set_network_anchoring_per_residue() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) set_network_state() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_new_chain_order() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_new_conformation() (pyrosetta.rosetta.core.pose.Pose method) set_new_energies_object() (pyrosetta.rosetta.core.pose.Pose method) set_new_final_stream() (pyrosetta.rosetta.basic.TracerImpl method) set_new_fold_tree_initializer() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_next_angle() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_next_correspondence() (pyrosetta.rosetta.utility.subset_mapping method) set_next_segment_id() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_nfrags() (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) set_nhits_per_match() (pyrosetta.rosetta.protocols.match.HitHasher method) set_niter() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) set_no_chainend_ter() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_no_design_cys() (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) set_no_detect_pseudobonds() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_no_filters() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_no_frags() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_no_optH() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_no_output_cen() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_no_stem_copy() (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) set_noncanonical_connection() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) set_nonideal() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_nonpivot_bb_torsion_id() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) set_nonpivot_res_to_sweep() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) set_nonpivot_torsion_sampling() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) set_normal() (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) set_normalization_function() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) set_normalize_to_thk() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_nrchi_prob_minimum_for_extra_samples() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_nread_limit_for_file() (pyrosetta.rosetta.utility.io.FileContentsMap method) set_nrepeat() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) set_nseq() (pyrosetta.rosetta.core.scoring.TMscoreStore method) set_nsteps() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) set_nstruct() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) set_nstruct_centroid() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method)

set_ntrial() (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) set_ntrials() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) set_nu() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_nu_true_range() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_nucleotide_to_A_form() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) set_num_cycles() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) set_num_geometric_constraints() (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_num_neighbors_counting_self_static() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) set_num_nodes() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) set_num_packs() (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) set_num_pose_minimize() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_num_random_samples() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_num_states_for_node() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_num_trials() (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) set_number_of_energy_sum_vertex_groups() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_nus() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_o2prime_legacy_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_obey_ENDMDL() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_occupied_space_bounding_box() (pyrosetta.rosetta.protocols.match.Matcher method) set_offset() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) set_omega() (pyrosetta.rosetta.core.pose.Pose method) set_omega0() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_omega0_copies_pitch_instead() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_omega1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_one_body_energy_for_node_state() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_only_stage4() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) set_open_mode() (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) set_optimize_cdrs() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_optimize_cyclic_threshold() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_optimize_memory_usage() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_options() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) set_orbital_icoor_id() (pyrosetta.rosetta.core.chemical.ResidueType method) set_orbital_xyz() (pyrosetta.rosetta.core.conformation.Residue method) set_original_pose() (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) set_original_scaffold_build_points() (pyrosetta.rosetta.protocols.match.Matcher method) set_original_scaffold_build_points_for_constraint() (pyrosetta.rosetta.protocols.match.Matcher method) set_originating_node_MPI_rank() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) set_other_pose_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) set_out() (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) set_outer_ca_only() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_outer_cycles() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_outer_max_distance() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_outer_sd() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_outer_unweighted_function() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_outer_use_harmonic_function() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_outer_weight() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_outlier_use() (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) set_output() (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) set_output_alternate_atomids() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_output_cluster_size() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_output_extra_RMSDs() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_output_file_name() (pyrosetta.rosetta.protocols.jobdist.BasicJob method) set_output_filename() (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) set_output_in_rosetta_num() (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) set_output_min_pose() (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) set_output_minimized_pose_list() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_output_name() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) set_output_pdb() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) set_output_period() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) set_output_pose_cache_data() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_output_pose_energies_table() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_output_res_and_chain() (in module pyrosetta.rosetta.core.pose) (in module pyrosetta.rosetta.core.pose.rna) set_output_secondary_structure() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_output_torsions() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_output_virtual() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_output_virtual_zero_occ() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_overall_aa_probabilities() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_overhang() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) set_overlap() (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) set_owner() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) set_pack_all_side_chains() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) set_pack_distance() (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) set_pack_input() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_pack_interface_separated() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) set_pack_missing_sidechains() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_pack_neighbors() (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) set_pack_o2prime_hydrogens() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) set_pack_protein_side_chains() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) set_pack_rounds() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) set_pack_separated() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) set_pack_shell() (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) set_pack_together() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) set_pack_weights() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_packer() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) set_packertask() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) set_parallel_weight() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_param_cache() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) set_param_from_options() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) set_param_index() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) set_parameter() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.MMAtomType method) set_paratope_cdrs() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_parent() (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap method) set_parin_favorite_output() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_partner() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) set_partners() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_path_option() (in module pyrosetta.rosetta.basic.options) set_path_vector_option() (in module pyrosetta.rosetta.basic.options) set_PBP_clustering_at_chain_closure() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_pdb_comments() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_pdb_parents() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_penalty() (pyrosetta.rosetta.core.scoring.MembraneEmbed method) set_pep_lengths() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_peptide_chain() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_per_chain_renumbering() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_perform_filters() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_perform_minimizer_run() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) set_perform_score_diff_cut() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_perform_VDW_rep_screen() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_perturb_CCD_off() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) set_perturb_cycles() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) set_perturb_KIC_off() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) set_perturb_show() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) set_perturb_temp() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) set_perturb_type() (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) set_perturbable() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_perturbation_magnitude() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_perturbation_type() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_perturber() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_perturber_effect() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) set_phi() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) set_phosphate() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) set_phosphate_domain() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) set_picked_positions() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_picking_rounds() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_piece() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) set_pivot_atoms() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_pivot_picker() (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) set_pivot_residue_selector() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_pivot_residues() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_pivots() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_placeholder() (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) set_polar_charge_cutoff() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_polymeric_connection() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) set_pool_name() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) set_population_based_conformer_sampling() (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) set_pos() (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) set_pos_in_owners_list() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) set_pos_list() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) set_pose() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) set_pose_after_closure() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) set_pose_and_scorefxn_for_edens_scoring() (in module pyrosetta.rosetta.protocols.electron_density) set_pose_energy() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) set_pose_from_broker() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) set_pose_no_initialize() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) set_pose_reactive_sites() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) set_pose_start() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_poses() (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) set_position() (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) set_positions_as_start_of_sequon() (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) set_preapply() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_precision() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) set_prefix() (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) set_prepack() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_presample_added_residue() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) set_presample_by_swa() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) set_preserve_atom_coords() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) set_preserve_crystinfo() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_preserve_datacache() (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) set_preserve_detailed_balance() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) set_preserve_header() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_preserve_whole_input_tag() (pyrosetta.rosetta.protocols.jobdist.BasicJob method) set_primary_cdrs() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_primary_strategy() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_print_out_info_to_pdb() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_prob() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) set_prob_random_pert_current() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) set_prob_sd_sampling() (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) set_prob_uniform() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) set_prob_withinrot() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) set_probability_data_cutoff() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) set_probe_radius() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_proc_id() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) set_ProCorrection_values_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_properties() (pyrosetta.rosetta.core.chemical.ResidueType method) set_property() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) set_protocol() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) set_protocol_and_batch_id() (in module pyrosetta.rosetta.protocols.features) set_protocol_info() (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) set_proton() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) set_proton_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) set_protonated_H1_adenosine_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_pseudobonds_to_residue() (pyrosetta.rosetta.core.conformation.Residue method) set_psi() (pyrosetta.rosetta.core.pose.Pose method) set_PyExitCallBack() (pyrosetta.rosetta.utility.py.PyExitCallback method) set_qsar_map() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) set_quench_mode() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) set_query_phi() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_query_phi_conf() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_query_profile() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_query_psi() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_query_psi_conf() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_query_sa() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_query_seq() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_quick_alignment() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_quota_score() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) set_r0() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_r1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_r_array() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) set_r_inv_array() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) set_radial_disp_ranges() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) set_radial_disps() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) set_radii_set() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) set_rama_check() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_rama_cutoff_energy() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) set_rama_prepro_mainchain_torsion_potential_name() (pyrosetta.rosetta.core.chemical.ResidueType method) set_rama_prepro_map_file_name() (pyrosetta.rosetta.core.chemical.ResidueType method) set_rama_prepro_multiplier() (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) set_rama_term_ramping() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_ramp_rama() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) set_ramp_vdw() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) set_random() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) set_random_confomer() (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) set_random_loop_flag() (pyrosetta.rosetta.protocols.LoopRebuild method) set_random_membrane_flip_angle() (pyrosetta.rosetta.protocols.membrane.FlipMover method) set_random_membrane_tilt_angle() (pyrosetta.rosetta.protocols.membrane.TiltMover method) set_random_order_() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) set_randomize1() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_randomize2() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_randomize_missing_coords() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_randomize_resnum() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_range() (pyrosetta.rosetta.protocols.membrane.FlipMover method) set_ranges_unmodifiable() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_rank_score() (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) set_rb_center() (pyrosetta.rosetta.core.kinematics.Jump method) set_rb_constraints() (in module pyrosetta.rosetta.protocols.rbsegment_relax) set_rb_delta() (pyrosetta.rosetta.core.kinematics.Jump method) set_rb_deltas() (pyrosetta.rosetta.core.kinematics.Jump method) set_read_fold_tree() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_read_only_ATOM_entries() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_read_pdb_header() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_real_option() (in module pyrosetta.rosetta.basic.options) set_real_vector_option() (in module pyrosetta.rosetta.basic.options) set_reasonable_fold_tree() (in module pyrosetta.rosetta.core.pose) set_rebuild_bulge_mode() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_recces_turner_mode() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_reconstruct() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) set_record_source() (pyrosetta.rosetta.core.io.silent.SilentFileData method) set_recover_low() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) set_recover_sidechains_filename() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_recovery_threshold() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) set_recursion_limit() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) set_reference_energy() (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) set_reference_pose() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) set_reference_pose_name() (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) set_refinable_lattice() (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) set_refine() (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) set_refine_pose_list() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) set_region() (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) set_reinitialize_CCD_torsions() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_relaxtype() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) set_relevant_atom_ids() (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) set_relevant_residues_mode() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) set_remember_unrecognized_res() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_remember_unrecognized_water() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_remove_any_set_forced_cluster() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_remove_cterminus_variant() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_remove_hydrogens() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_remove_nterminus_variant() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_remove_target_types() (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) set_rename_tags() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_renumber_pdb() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_repack() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) set_repack_list() (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) set_repack_period() (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) set_repack_separated() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) set_repeat_tail_length() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) set_repeating_unit_offset() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_repeats() (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) set_report_all_heavy_atom_unsats() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_report_all_unsats() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_report_as() (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) set_report_bb_heavy_atom_unsats() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_report_crd() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) set_report_format() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_report_nonheavy_unsats() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_report_sc_heavy_atom_unsats() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_reporting() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_repulsive_term_ramping() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_require_mm_bend() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_required_connections_for_residue() (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) set_res1() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) set_res2() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) set_res_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) set_res_name() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) set_res_type_set() (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) set_rescoords() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) set_rescore_only() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) set_reset_filters() (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) set_reset_mode() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) set_resfile() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) set_resfile_1() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_resfile_2() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_resid() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.moves.ResId method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) set_residue() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_residue_base2_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_residue_base_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_residue_mapping() (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) set_residue_name3() (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) set_residue_names() (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) set_residue_numbers() (pyrosetta.rosetta.core.io.silent.SilentStruct method) set_residue_pair_xform() (in module pyrosetta.rosetta.core.scoring.motif) set_residue_range() (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) set_residue_range_not_surface() (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) set_residue_sampling_from_pose_and_movemap() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_residue_selector() (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.TotalEnergyMetric method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation method) set_residue_selector1() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_residue_selector2() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_residue_selector_reference() (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) set_residue_subset() (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) set_residue_surface_cutoff() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_residue_type() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) set_residue_type_set_mode() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_residues() (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation method) set_residues_for_atom_name_remapping() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_residues_per_repeat() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_resinfo() (pyrosetta.rosetta.core.pose.PDBInfo method) set_resnum() (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_resnum_string() (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) set_restrict_only_design_to_loops() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) set_restrict_partners_to_chains() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_restrict_receptors_to_chains() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_restrictions_aa() (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) set_restrictions_append() (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) set_restrictions_exclude() (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) set_restype() (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) set_restype_index() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) set_rigid_body_confs() (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) set_rigid_body_mover() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_ring_conformation() (pyrosetta.rosetta.core.pose.Pose method) set_rm_virt_phosphate() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_rms_group_cutoff() (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) set_rmsd() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) set_rmsd_cutoff() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_rmsd_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_rmsd_type() (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) set_rna_legacy_output_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_rna_secstruct_legacy() (in module pyrosetta.rosetta.core.pose.rna.secstruct_legacy) set_root() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) set_root_at_first_rigid_body() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_root_atom() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) set_roots() (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) set_rot_magnitude() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) set_rotamer_operation() (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) set_rotamer_sampling_data_for_RLT() (in module pyrosetta.rosetta.core.pack.task.operation) set_rotamer_set_operation() (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) set_rotation() (pyrosetta.rosetta.core.kinematics.Jump method) set_rotation_magnitude() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_rotation_range() (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) set_rotation_std_dev() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_rottrial() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_rounds() (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) set_rsd_set() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) set_rsd_type_name3() (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) set_rsd_type_set() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_rt_min() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_run_relax() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) set_run_snugdock() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) set_rv_infos() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) set_safe() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_sample_all_chi() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sample_beta() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sample_both_sugar_base_rotamer() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_sample_cis_pro_frequency() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_sample_index() (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) set_sample_level() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_sample_nonpivot_torsions() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_sample_ONLY_multiple_virtual_sugar() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sample_pH() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) set_sample_range_large() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) set_sample_range_small() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) set_sample_startegy_for_constraint() (pyrosetta.rosetta.protocols.match.Matcher method) set_sample_strategy_for_chi() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) set_sample_type() (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) set_sample_zero_probs_at() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_sampler() (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) set_sampler_assert_no_virt_sugar_sampling() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sampler_extra_beta_rotamer() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sampler_extra_epsilon_rotamer() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sampler_gaussian_stdev() (in module pyrosetta.rosetta.protocols.recces) set_sampler_include_torsion_value_in_tag() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sampler_max_centroid_distance() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sampler_num_pose_kept() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sampler_perform_phosphate_pack() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sampler_silent_file() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sampler_try_sugar_instantiation() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_samples() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_sampletype() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_sampling_temperature() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) set_sasa_cutoff() (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) set_sc_min() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_sc_neighbor_denominator() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_sc_neighbor_dist_midpoint() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_scaffold_flexibility() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_scheme_conversion() (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) set_score() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.optimization.Particle method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) set_score_against_internal_contacts() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_score_component() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) set_score_cutoff() (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) set_score_diff_cut() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_score_filter() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) set_score_function() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) set_score_fxn() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_score_margin() (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) set_score_threshold() (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) set_score_type() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_score_weight() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) set_scorefunction() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.TotalEnergyMetric method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) set_scorefunction_min() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) set_scorefxn() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) set_scorefxn_deriver() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_scorefxn_design() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_scorefxn_low() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_scorefxn_min() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) set_scorefxn_minimize() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) set_scorefxn_pack() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) set_scorefxn_relax() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_scorefxn_repack() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) set_scoretype() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) set_scoretypes() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) set_sd() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) set_sd_ang() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) set_sd_degree() (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) set_sd_dih() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) set_sd_dis() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) set_sd_range() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_seal_foldtree() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) set_search_paths() (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) set_second_expression() (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) set_secondary_residue_selector() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) set_secstruct() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.rna.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_secstruct_from_bp() (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) set_secstruct_from_dssp() (in module pyrosetta.rosetta.protocols.loops) set_secstruct_from_psipred_ss2() (in module pyrosetta.rosetta.protocols.loops) set_seed() (pyrosetta.rosetta.numeric.random.RandomGenerator method) set_segdef() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) set_segment() (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) set_segment1_ids() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) set_segment2_ids() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) set_segment_IDs() (pyrosetta.rosetta.core.io.silent.SilentStruct method) set_select_designable() (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) set_select_fixed() (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) set_select_from_branch_residue() (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) set_select_from_branch_residues() (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) set_select_in_membrane() (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector method) set_select_only_alpha_aas() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) set_select_only_FAMILYVW() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) set_select_packable() (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) set_select_positive_phi() (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) set_selector() (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) set_selector_type() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) set_separate_prt_ligand() (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) set_seq_design_cdrs() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_seq_design_options() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_seq_sep_scale() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_seqmap() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) set_seqprof() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) set_sequence() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) set_set_up_metal_bonds() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_sfxn() (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_sfxn_cycles() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_shadowing_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) set_shared_silent_data() (pyrosetta.rosetta.core.io.silent.SilentFileData method) set_sheet() (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) set_sheet_topology() (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) set_sheetlist() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) set_sheetlist_as_is() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) set_short_backrub_mover() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_show_accessed_options_flag() (pyrosetta.rosetta.utility.options.OptionCollection method) set_show_all_fixes() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_show_unused_options_flag() (pyrosetta.rosetta.utility.options.OptionCollection method) set_show_viol_level() (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) set_sidechain() (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_sidechain_frlx_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_silent_file() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) set_silent_file_data() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_silent_file_name() (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) set_silent_files_in() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_silentout_file_name() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) set_sim() (pyrosetta.rosetta.protocols.cluster.APCluster method) set_simple_append_map() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_simple_metric() (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_simple_metrics() (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) set_single_loop_fold_tree() (in module pyrosetta.rosetta.protocols.forge.methods) (in module pyrosetta.rosetta.protocols.loops) set_single_resnum() (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) set_size_and_nbb() (pyrosetta.rosetta.protocols.frags.TorsionFragment method) set_skip_chi_min() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) set_skip_clustering() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_skip_complicated_stuff() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_skip_connect_info() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_skip_coord_constraints() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_skip_minimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_skip_reporting() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_skip_sampling() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_skip_set_reasonable_fold_tree() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_skip_stage1() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) set_skip_stage2() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) set_slice_res() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) set_solution_picker() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) set_sorter() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) set_source_size() (pyrosetta.rosetta.utility.subset_mapping method) set_span() (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) set_sparse_aa_info_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_special_edges() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) set_species() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) set_spin() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_ss() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_ss_cutoff() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_ss_from_phipsi() (in module pyrosetta.rosetta.core.pose) set_ss_from_str() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) set_ss_lowstrand() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_ssid() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) set_SSorient() (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) set_stage2_cycles() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_stage2_repack_period() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_stage3_cycles() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_stage4_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) set_start() (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) set_start_added_residue_in_aform() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) set_start_rep_weight() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_start_res() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_start_segments() (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) set_starting_reference_energies() (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) set_starting_rep() (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) set_state_for_node() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_stats_cutoff() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_status() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) set_status_prefix() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) set_status_suffix() (pyrosetta.rosetta.protocols.jd3.LarvalJob method) set_stem_size() (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) set_step_size() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_stepwise_modeler() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) set_stop() (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.protocols.loops.Loop method) set_stop_after_closure() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_stop_res() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_stop_sampling() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_stop_segments() (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) set_strand_dist_cutoff() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_strand_extensions() (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) set_strand_strand_weights() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_strategy() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_stretch_strand_dist_cutoff() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_strict_looprelax_checks() (pyrosetta.rosetta.protocols.loops.Loops method) set_strict_loops() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) set_stride() (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) set_string_option() (in module pyrosetta.rosetta.basic.options) set_string_vector_option() (in module pyrosetta.rosetta.basic.options) set_strip_existing_glycans() (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) set_struct_ids_from_sql() (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) set_struct_ids_from_strings() (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) set_stub_transform() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) set_subelements_pick_one() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) set_subelements_pick_one_or_none() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) set_subelements_repeatable() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) set_subelements_single_appearance_optional() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) set_subelements_single_appearance_required() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) set_subelements_single_appearance_required_and_ordered() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) set_submotif_library() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) set_subset() (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) set_suffix() (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) set_sugar() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) set_sugar_domain() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) set_suite_cluster_radius() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_super_secret_fixed_interface_mode() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_superimpose_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_suppress_checkpoints() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_suppress_zero_occ_pdb_output() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_sweep_nonpivot_torsions() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_sweep_nsteps() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) set_sweep_start_angle() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) set_sweep_step_size() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) set_sym_dof_names() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) set_symm_count() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_symm_repeats() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) set_symm_type() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_symmetric_sequence() (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) set_symmetry() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) set_tag_from_pose() (pyrosetta.rosetta.core.io.silent.SilentStruct method) set_takeoff_domain() (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) set_takeoff_pos() (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) set_targ_ang() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_targ_dih() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_target() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) set_target_atom_name() (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) set_target_geomcst_id() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) set_target_range() (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) set_target_res() (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) set_target_res_index() (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) set_target_res_pdb() (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) set_target_residue() (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) set_target_type() (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) set_task() (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) set_task_and_movemap() (in module pyrosetta.rosetta.protocols.hydrate) set_task_factory() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) set_task_scaling() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_task_with_de_novo_water_using_resfile() (in module pyrosetta.rosetta.protocols.hydrate) set_taskfactory() (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) set_tau() (pyrosetta.rosetta.core.conformation.Residue method) set_temp() (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) set_temp_cycles() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_temperature() (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) set_temperature_observer() (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) set_temperature_ramping() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_temperature_schedule() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_tempering() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) set_template_pose() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_template_res_index() (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) set_temps() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_terminal_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_test_all_mg_hydration_frames() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_tether_jump() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_thermal_sampler_output_min_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_theta() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) (pyrosetta.rosetta.core.pose.Pose method) set_threshold() (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) set_throw_on_double_registration() (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) set_tilt() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_tilt1_center() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_tilt2_center() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_tmh_jump() (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) set_to_origin() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) set_to_pose() (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) set_tolerance() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_tolerated_overlap() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_tor_U1D3_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_tor_U2D2_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_tor_U3D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_torsion() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) set_torsion_angle() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) set_torsion_to_pose() (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) set_torsion_type() (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) set_total_energy_cutoff() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_total_jobs() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) set_total_residue() (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) set_total_score_last_considered() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) set_total_weight() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) set_tracer_options() (pyrosetta.rosetta.basic.TracerImpl method) set_traits() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) set_traits_size() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) set_trans_magnitude() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) set_translation() (pyrosetta.rosetta.core.kinematics.Jump method) set_translation_magnitude() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_trim_info() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) set_turn_off_rna_chem_map_during_optimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_two_stage_clustering() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_type() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) set_unbound_mode() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_uniform_backrub() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_uniform_euler_angle_bin_width() (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) set_uniform_sd_sampling() (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) set_uniform_trans() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_uniform_xyz_bin_width() (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) set_unweighted_function() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) set_up_mapfile_reassignments_from_commandline() (in module pyrosetta.rosetta.core.chemical) set_up_metal_bonds() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_up_metal_constraints() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_up_quota_nnmake_style() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_up_residuearrayannealableenergy_for_packing() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) set_up_ss_abego_quota() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_up_target_sequence() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) set_up_voxel_grid_and_compute_burial() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) set_update_boinc() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) set_update_polymer_bond_dependent_atoms() (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) set_update_polymer_dependent() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) set_upper_connect_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) set_upper_residues() (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) set_upper_segment() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_upper_threshold() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_upper_value() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_upstream_pose() (pyrosetta.rosetta.protocols.match.Matcher method) set_use_basic_enhanced_n_linked_sequon() (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) set_use_big_polar_hydrogen() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) set_use_centroid_dG() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_use_cluster_csts() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_use_cluster_for_H3() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_use_conformer_population_stats() (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) set_use_constraints() (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) set_use_contact_selector() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_use_coordinate_constraints() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) set_use_ddG_style() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_use_defaults() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_use_delta() (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) set_use_dssp_reduced() (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) set_use_ellipsoidal_randomization() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_use_epitope_constraints() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_use_general_csts_on_cluster_failure() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_use_green_packer() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_use_harmonic_function() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) set_use_hbnet_behavior() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_use_increased_vdw_radii() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) set_use_jobname() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_use_legacy_protocol() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_use_ligand_selector() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_use_nblist() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) set_use_outliers() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_use_packer_instead_of_rotamer_trials() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) set_use_pdb_format_HETNAM_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_use_phenix_geo() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_use_rama2b() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) set_use_rama_prepro_for_sampling() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_use_reporter_behavior() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_use_resfile() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_use_sc_neighbors() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_use_secondary_graft_mover_if_needed() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_use_seqprof_constraints() (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) set_use_sugar_bb_data_if_needed() (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) set_use_three_letter_code() (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) set_use_tracer() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) set_use_vsasa() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_user_chain1() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) set_user_chain2() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) set_user_defined_name() (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_user_input_VDW_bin_checker() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_user_provided_movers() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) set_using() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) set_using_a_resselect() (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) set_valid() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) set_valid_energies() (pyrosetta.rosetta.core.io.silent.SilentStruct method) set_vall() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_value() (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) set_variant_type() (pyrosetta.rosetta.core.chemical.ResidueProperties method) set_vary_bondangles() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_vary_ca_bond_angles() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) set_vary_polar_hydrogen_geometry() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_vary_rna_bond_geometry() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_vdw_cached_rep_screen_info() (in module pyrosetta.rosetta.protocols.scoring) set_vdw_cached_rep_screen_info_from_pose() (in module pyrosetta.rosetta.protocols.scoring) set_vdw_calculation_annotated_sequence() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) set_VDW_rep_alignment_RMSD_CUTOFF() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_VDW_rep_delete_matching_res() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_VDW_rep_screen_info() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_VDW_rep_screen_physical_pose_clash_dist_cutoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_VDW_weight() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_verbose() (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) set_verbose_sampler() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_vertex_member_of_group() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_view() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_virtual_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) set_virtual_sugar_do_minimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_virtual_sugar_do_screens() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_virtual_sugar_keep_base_fixed() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_virtual_sugar_legacy_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_virtualize_packable_moieties_in_screening_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_vlb() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) set_voxel_size_and_padding() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) set_water_info_and_add_de_novo_water() (in module pyrosetta.rosetta.protocols.hydrate) set_weak_pointer_to_self() (pyrosetta.rosetta.core.kinematics.AtomTree method) set_weight() (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) set_weight_constraints_NtoC() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_weight_constraints_sheet() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_weight_if_zero() (pyrosetta.rosetta.core.scoring.ScoreFunction method) set_weights() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_width() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) set_window_size() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) set_working_moving_res_list() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) set_working_pack_res() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) set_working_parameters() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_working_parameters_exist() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_write_all_connect_info() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_write_glycan_pdb_codes() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_write_no_structures() (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) set_write_pdb_link_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_write_pdb_parametric_info() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_write_separate_scorefile() (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) set_wt_pose() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) set_wu_type() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) set_x_standard_deviations() (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) set_xyz() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.pose.Pose method) set_xyz_bin_widths() (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) set_z0_offset() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_z1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_z1_offset() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_zero_prob_weight_at() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) set_zeta() (pyrosetta.rosetta.core.pose.Pose method) setall() (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) SetAllAtomsRepulsive (class in pyrosetta.rosetta.core.chemical) SetAtomicCharge (class in pyrosetta.rosetta.core.chemical) SetAtomTree (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) SetAtomType (class in pyrosetta.rosetta.core.chemical) setB() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetBackboneHeavyatom (class in pyrosetta.rosetta.core.chemical) SetCatalyticResPackBehavior (class in pyrosetta.rosetta.protocols.enzdes) setCenterOnMiddleCA() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetChiMover (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) setClusterOversamp() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setClusterRadius() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setConvoluteSingleR() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setDelR() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setDoRefine() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetFormalCharge (class in pyrosetta.rosetta.core.chemical) setFragDens() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setGridStep() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetICoor (class in pyrosetta.rosetta.core.chemical) SetInterchangeabilityGroup_String (class in pyrosetta.rosetta.core.chemical) SetIO_String (class in pyrosetta.rosetta.core.chemical) setLaplacianOffset() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setMaxRotPerTrans() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetMembraneCenterMover (class in pyrosetta.rosetta.protocols.membrane) SetMembraneCenterMoverCreator (class in pyrosetta.rosetta.protocols.membrane) SetMembraneNormalMover (class in pyrosetta.rosetta.protocols.membrane) SetMembraneNormalMoverCreator (class in pyrosetta.rosetta.protocols.membrane) SetMembranePositionMover (class in pyrosetta.rosetta.protocols.membrane) SetMembranePositionMoverCreator (class in pyrosetta.rosetta.protocols.membrane) setMinBackbone() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setMinDist() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetMMAtomType (class in pyrosetta.rosetta.core.chemical) setNames() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) setNative() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetNbrAtom (class in pyrosetta.rosetta.core.chemical) SetNbrRadius (class in pyrosetta.rosetta.core.chemical) setNCyc() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setNeighbors() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) SetNetFormalCharge (class in pyrosetta.rosetta.core.chemical) setNormScores() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setNRsteps() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetOrientAtom (class in pyrosetta.rosetta.core.chemical) setOutputSilent() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setPassThrough() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setPdbCodes() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) setPointRadius() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetPolymerConnectAtom (class in pyrosetta.rosetta.core.chemical) setPoseExtraScore() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) SetResidueAliasMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) setResidueRange() (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) SetSDFType() (pyrosetta.rosetta.core.chemical.Bond method) setSecStruct() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) setSeed() (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) setSymminfo() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setTag() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetTemperatureFactor (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) setTopN() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetTorsion (class in pyrosetta.rosetta.protocols.simple_moves) SetToType() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) setup() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) setup_A_LH_foldtree() (in module pyrosetta.rosetta.protocols.antibody) setup_after_edge_addition() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) setup_alignment_map() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) setup_atom_id_map() (in module pyrosetta.rosetta.core.pose.copydofs) setup_atom_id_map_match_atom_names() (in module pyrosetta.rosetta.core.pose.copydofs) setup_atom_type_reassignments_from_commandline() (in module pyrosetta.rosetta.core.chemical) setup_atomic_charge_reassignments_from_commandline() (in module pyrosetta.rosetta.core.chemical) setup_attlist_for_derived_classes() (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) setup_base_pair_constraints() (in module pyrosetta.rosetta.core.pose.rna) setup_bulge_jump_point() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) setup_CDR_cluster() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) setup_CDR_clusters() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) setup_centroid_constraints() (in module pyrosetta.rosetta.protocols.hybridization) setup_centroid_scatter() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) setup_centroid_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) setup_chain_break_jump_point() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) setup_chain_break_variants() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) setup_chainbreak_variants() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) setup_coarse_chainbreak_constraints() (in module pyrosetta.rosetta.protocols.rna.denovo) setup_conformer_map() (in module pyrosetta.rosetta.protocols.motifs) setup_connectivity() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) setup_constraints() (in module pyrosetta.rosetta.protocols.hybridization) setup_convergence_checks_from_cmdline() (in module pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks) setup_copy_DOF_input() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) setup_corresponding_atoms() (in module pyrosetta.rosetta.core.conformation) setup_cylindrical_coords() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) setup_default_evaluators() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) setup_disconnected() (in module pyrosetta.rosetta.protocols.rbsegment_relax) setup_dof_mask_from_move_map() (in module pyrosetta.rosetta.core.pose) setup_dof_to_torsion_map() (in module pyrosetta.rosetta.core.pose) setup_element2name() (in module pyrosetta.rosetta.core.chemical.element) setup_empty_config() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) setup_filter_stats() (in module pyrosetta.rosetta.protocols.ncbb) setup_fold() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) setup_fold_tree() (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) setup_fold_tree_and_jumps_and_variants() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) setup_foldtree() (in module pyrosetta.rosetta.protocols.docking) setup_foldtree_around_anchor_invrot() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) setup_foldtree_from_anchors() (in module pyrosetta.rosetta.protocols.membrane) setup_foldtree_pose_com() (in module pyrosetta.rosetta.protocols.membrane) setup_for_density_scoring() (in module pyrosetta.rosetta.core.import_pose) setup_for_derivatives() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.FACTSPotential method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) setup_for_derivatives_for_residue() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) setup_for_derivatives_for_residue_pair() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) setup_for_dna() (in module pyrosetta.rosetta.protocols.relax) setup_for_lr2benmeth_minimization_for_respair() (pyrosetta.rosetta.core.scoring.ScoreFunction method) setup_for_minimizing() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) setup_for_minimizing_for_node() (pyrosetta.rosetta.core.scoring.ScoreFunction method) setup_for_minimizing_for_residue() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) setup_for_minimizing_for_residue_pair() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) setup_for_minimizing_sr2b_enmeths_for_minedge() (pyrosetta.rosetta.core.scoring.ScoreFunction method) setup_for_packing() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.FACTSPotential method) (pyrosetta.rosetta.core.scoring.GenBornPotential method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) setup_for_residue_pair_energies() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) setup_for_sampling() (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction method) setup_for_scoring() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.FACTSPotential method) (pyrosetta.rosetta.core.scoring.GenericBondedPotential method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) setup_for_scoring_for_residue() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) setup_for_scoring_for_residue_energy_methods() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) setup_for_scoring_for_residue_pair() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) setup_form_factors() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) setup_fragment_picker() (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) setup_from_kill_hairpins_file() (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) setup_from_psipred() (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) setup_from_rotamer_dots() (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) setup_full_model_info() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) setup_fullatom_constraints() (in module pyrosetta.rosetta.protocols.hybridization) setup_glycan_nodes() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) setup_glycan_trees() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) setup_icoor_reassignments_from_commandline() (in module pyrosetta.rosetta.core.chemical) setup_info() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) setup_jumps() (in module pyrosetta.rosetta.core.import_pose) setup_kic_config() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) setup_kic_with_fragments_config() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) setup_killhairpins() (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) setup_LH_A_foldtree() (in module pyrosetta.rosetta.protocols.antibody) setup_list() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) setup_loophash_kic_config() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) setup_matching_atoms_with_given_names() (in module pyrosetta.rosetta.core.scoring) setup_matching_CA_atoms() (in module pyrosetta.rosetta.core.scoring) setup_matching_heavy_atoms() (in module pyrosetta.rosetta.core.scoring) setup_matching_protein_backbone_heavy_atoms() (in module pyrosetta.rosetta.core.scoring) setup_membrane_topology() (in module pyrosetta.rosetta.protocols.relax) setup_min_map() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) setup_movemap() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) setup_native_pose() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) setup_options_for_VDW_bin_checker() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) setup_packer() (in module pyrosetta.rosetta.protocols.mpi_refinement) setup_packer_and_movemap() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) setup_packer_task() (in module pyrosetta.rosetta.protocols.antibody) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) setup_parallel_antiparallel_weights() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) setup_pert_foldtree() (in module pyrosetta.rosetta.protocols.ncbb) setup_pose_from_rbsegs() (in module pyrosetta.rosetta.protocols.rbsegment_relax) setup_pose_input_stream() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) setup_pose_rbsegs_keep_loops() (in module pyrosetta.rosetta.protocols.rbsegment_relax) setup_pose_setup_class() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) setup_pose_with_moving_residue_alternative_list() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body) setup_protein_backbone_atom_id_map() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) setup_rmsd_atom_names() (in module pyrosetta.rosetta.protocols.analysis.simple_metrics) setup_rna_working_parameters() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) setup_rsdtype() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) setup_sampler() (in module pyrosetta.rosetta.protocols.stepwise.sampler.rna) setup_simple_fold_tree() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) setup_simple_full_length_rna_working_parameters() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) setup_single_loop_double_arm_remodeling_foldtree() (in module pyrosetta.rosetta.protocols.grafting) setup_single_loop_single_arm_remodeling_foldtree() (in module pyrosetta.rosetta.protocols.grafting) setup_star_topology() (in module pyrosetta.rosetta.protocols.rbsegment_relax) setup_suite_atom_id_map() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) setup_symmetric_conformation() (in module pyrosetta.rosetta.core.conformation.symmetry) setup_three_prime_phosphate_based_on_next_residue() (in module pyrosetta.rosetta.core.pose.rna) setup_unified_stepwise_modeler() (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) setup_user_coordinate_constraints() (in module pyrosetta.rosetta.protocols.hybridization) setup_user_defined_jumps() (in module pyrosetta.rosetta.core.import_pose) setup_vall_cheating_fragments() (in module pyrosetta.rosetta.protocols.frags) setup_vall_fragments() (in module pyrosetta.rosetta.protocols.frags) setup_vary_polar_hydrogen_geometry() (in module pyrosetta.rosetta.protocols.simple_moves) setup_vary_rna_bond_geometry() (in module pyrosetta.rosetta.protocols.simple_moves) setup_vdw_cached_rep_screen_info() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) setup_water_bank_for_magnesiums() (in module pyrosetta.rosetta.core.import_pose) setup_working_parameters_explicit() (in module pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters) setup_working_parameters_for_swa() (in module pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters) SetupForFibrilMover (class in pyrosetta.rosetta.protocols.fibril) SetupForSymmetryMover (class in pyrosetta.rosetta.protocols.symmetry) SetupMetalsMover (class in pyrosetta.rosetta.protocols.simple_moves) SetupNCSMover (class in pyrosetta.rosetta.protocols.symmetry) SetupRamaTables() (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) SetVirtualShadow (class in pyrosetta.rosetta.core.chemical) sever_chemical_bond() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) SewGraph (class in pyrosetta.rosetta.protocols.legacy_sewing) sfd_req_1benmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationNode method) sfd_req_1benmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationNode method) sfd_req_2benmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) sfd_req_2benmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) sformat_idxof() (in module pyrosetta.rosetta.numeric.random) sfr() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) sfs_dm_req_1benmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationNode method) sfs_dm_req_1benmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationNode method) sfs_dm_req_2benmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationNode method) sfs_dm_req_2benmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationNode method) sfs_drs_req_enmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationNode method) sfs_drs_req_enmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationNode method) sfs_req_2benmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) sfs_req_2benmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) sgn() (in module pyrosetta.rosetta.core.io.pose_from_sfr) ShapeComplementarityCalculator (class in pyrosetta.rosetta.core.scoring.sc) ShapeComplementarityCalculatorException (class in pyrosetta.rosetta.core.scoring.sc) share_axis_atoms() (in module pyrosetta.rosetta.core.scoring.power_diagram) shared_from_this() (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringIntegerMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) SharedSilentDataType (class in pyrosetta.rosetta.core.io.silent) ShearFreePeptideMover (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers) ShearMinCCDTrialCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) ShearMover (class in pyrosetta.rosetta.protocols.simple_moves) sheet_fraction() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) SheetBuilder (class in pyrosetta.rosetta.protocols.jumping) SheetDB (class in pyrosetta.rosetta.protocols.denovo_design.components) SheetFoldType (class in pyrosetta.rosetta.protocols.fldsgn.topology) SheetFoldTypeManager (class in pyrosetta.rosetta.protocols.fldsgn.topology) SHEETInformation (class in pyrosetta.rosetta.core.io) SHEETInformations() (pyrosetta.rosetta.core.io.StructFileRep method) SheetRemodelConstraintGenerator (class in pyrosetta.rosetta.protocols.fldsgn) SheetTranslate (class in pyrosetta.rosetta.protocols.nonlocal) shell_radius_for_atom() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) shift() (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) shift_by() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) shift_jump_numbers_in_dofs() (in module pyrosetta.rosetta.core.conformation.symmetry) shift_jumps() (in module pyrosetta.rosetta.protocols.forge.methods) shift_to() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) short_desc() (pyrosetta.rosetta.core.pose.PDBInfo method) short_description() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) short_frag_cycle_ratio() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) short_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) short_ss_loop_filter() (in module pyrosetta.rosetta.protocols.evolution.AlignmentCleanerTools) shortd() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) ShortToRealAngle() (in module pyrosetta.rosetta.protocols.loophash) show() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Atom method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.DipolarCoupling method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) (pyrosetta.rosetta.protocols.jumping.SameStrand method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) (pyrosetta.rosetta.protocols.mean_field.ResHashMap method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) (pyrosetta.rosetta.utility.excn.BadInput method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) show_accessed_options() (pyrosetta.rosetta.utility.options.OptionCollection method) show_additional() (pyrosetta.rosetta.core.scoring.ScoreFunction method) show_additional_info() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) show_all() (pyrosetta.rosetta.utility.options.OptionCollection method) show_all_atom_names() (pyrosetta.rosetta.core.chemical.ResidueType method) show_all_fixes() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) show_all_hier() (pyrosetta.rosetta.utility.options.OptionCollection method) show_all_residue_tasks() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) show_atom_tree() (in module pyrosetta.rosetta.core.conformation) show_availability() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) show_base_pair_params() (in module pyrosetta.rosetta.core.scoring.dna) show_classic() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) show_cluster_assignments() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) show_counters() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) show_def() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) show_definition() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) show_definitions() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) show_dna_geometry() (in module pyrosetta.rosetta.core.scoring.dna) show_foldtree() (in module pyrosetta.rosetta.core.conformation.symmetry) show_header() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) show_help() (pyrosetta.rosetta.utility.options.OptionCollection method) show_help_hier() (pyrosetta.rosetta.utility.options.OptionCollection method) show_if_nonzero_weight() (pyrosetta.rosetta.core.scoring.EMapVector method) show_inaccessed_user_options() (pyrosetta.rosetta.utility.options.OptionCollection method) show_internals() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) show_line() (pyrosetta.rosetta.core.scoring.ScoreFunction method) show_line_headers() (pyrosetta.rosetta.core.scoring.ScoreFunction method) show_new_base_step_params() (in module pyrosetta.rosetta.core.scoring.dna) show_nonzero() (pyrosetta.rosetta.core.scoring.EMapVector method) show_numbers() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) show_option_help() (pyrosetta.rosetta.utility.options.OptionCollection method) show_option_help_hier() (pyrosetta.rosetta.utility.options.OptionCollection method) show_params() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) show_pdb_ids() (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) show_pretty() (pyrosetta.rosetta.core.scoring.ScoreFunction method) show_rdc_values() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) show_residue_connections() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) show_residue_task() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) show_scorefxn_weight_lines() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) show_scores() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) show_scoring_methods() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) show_state() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) show_submotif_info_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) show_table_text() (pyrosetta.rosetta.utility.options.OptionCollection method) show_table_Wiki() (pyrosetta.rosetta.utility.options.OptionCollection method) show_tensor_matrix() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) show_tensor_stats() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) show_tensor_stats_nls() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) show_time() (in module pyrosetta.rosetta.basic) show_total_headers() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) show_totals() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) show_unmoved() (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged method) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged method) show_unused_options() (pyrosetta.rosetta.utility.options.OptionCollection method) show_user() (pyrosetta.rosetta.utility.options.OptionCollection method) show_valid() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) show_violations() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) show_water_hb_network() (in module pyrosetta.rosetta.protocols.hydrate) show_weighted() (pyrosetta.rosetta.core.scoring.EMapVector method) ShowHState (class in pyrosetta.rosetta.protocols.viewer.graphics_states_param) shrink() (pyrosetta.rosetta.protocols.frags.VallData method) shrink_to_fit() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) shuffle() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) shutdown() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) sidechain() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) sidechain_frlx_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) sidechain_sidechain_energy() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) sidechainAtoms_begin() (pyrosetta.rosetta.core.conformation.Residue method) SidechainContactDistCutoff (class in pyrosetta.rosetta.protocols.frag_picker) SidechainMCMover (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) SidechainMetropolisHastingsMover (class in pyrosetta.rosetta.protocols.canonical_sampling) SidechainMetropolisHastingsMoverCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) SidechainMover (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) SidechainMoverBase (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) SidechainStateAssignment (class in pyrosetta.rosetta.core.pack.scmin) sigma1() (pyrosetta.rosetta.core.scoring.CSA method) sigma2() (pyrosetta.rosetta.core.scoring.CSA method) sigma3() (pyrosetta.rosetta.core.scoring.CSA method) Sigmoid (class in pyrosetta.rosetta.protocols.calc_taskop_filters) sigmoid_filter() (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) sign() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.ObjexxFCL) signature_string() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) silent() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) silent_energies() (pyrosetta.rosetta.core.io.silent.SilentStruct method) silent_Es() (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) silent_file() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) silent_file_data() (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) silent_in() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) silent_out() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) silent_struct_output_list() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) SilentEnergy (class in pyrosetta.rosetta.core.io.silent) SilentFileData (class in pyrosetta.rosetta.core.io.silent) SilentFileHeaderLine (class in pyrosetta.rosetta.core.io.silent) SilentFileJobInputter (class in pyrosetta.rosetta.protocols.jd2) SilentFileJobOutputter (class in pyrosetta.rosetta.protocols.jd2) SilentStruct (class in pyrosetta.rosetta.core.io.silent) SilentStructCreator (class in pyrosetta.rosetta.core.io.silent) SilentTrajectoryRecorder (class in pyrosetta.rosetta.protocols.canonical_sampling) SilentTrajectoryRecorderCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) SIMPLE_CYCPEP_PREDICT_MPI_SORT_TYPE (class in pyrosetta.rosetta.protocols.cyclic_peptide_predict) simple_element_naming_func_has_been_set() (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) simple_fold_tree() (in module pyrosetta.rosetta.protocols.antibody) (in module pyrosetta.rosetta.protocols.antibody_legacy) (in module pyrosetta.rosetta.protocols.star) simple_ft() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) simple_mapping_from_file() (in module pyrosetta.rosetta.core.sequence) simple_metric_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.SimpleMetricLoader method) simple_numeric_deriv_check() (in module pyrosetta.rosetta.core.optimization) simple_one_loop_fold_tree() (in module pyrosetta.rosetta.protocols.antibody) (in module pyrosetta.rosetta.protocols.antibody_legacy) simple_rmsd_cutoff_relax() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) simple_tree() (pyrosetta.rosetta.core.kinematics.FoldTree method) simple_visualize_fold_tree() (in module pyrosetta.rosetta.core.kinematics) simple_visualize_fold_tree_and_movemap() (in module pyrosetta.rosetta.core.kinematics) simple_visualize_fold_tree_and_movemap_bb_chi() (in module pyrosetta.rosetta.core.kinematics) SimpleCycpepPredictApplication (class in pyrosetta.rosetta.protocols.cyclic_peptide_predict) SimpleCycpepPredictApplication_MPI_JobResultsSummary (class in pyrosetta.rosetta.protocols.cyclic_peptide_predict) SimpleGlycosylateMover (class in pyrosetta.rosetta.protocols.carbohydrates) SimpleHbondsToAtomFilter (class in pyrosetta.rosetta.protocols.simple_filters) SimpleInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) SimpleMetric (class in pyrosetta.rosetta.core.simple_metrics) SimpleMetricFeaturesCreator (class in pyrosetta.rosetta.protocols.features) SimpleMetricFilter (class in pyrosetta.rosetta.protocols.simple_filters) SimpleMetricLoader (class in pyrosetta.rosetta.protocols.parser) SimpleThreadingMover (class in pyrosetta.rosetta.protocols.simple_moves) simplifyWhiteSpace() (in module pyrosetta.rosetta.protocols.sparta) simulate_mpi() (pyrosetta.rosetta.utility.SimulateMPI method) simulate_mpi_message_type (class in pyrosetta.rosetta.utility) SimulatedTempering (class in pyrosetta.rosetta.protocols.canonical_sampling) SimulatedTemperingCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) SimulateMPI (class in pyrosetta.rosetta.utility) simultaneous_cycles() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) sin_cos_range() (in module pyrosetta.rosetta.numeric) SINFXN() (in module pyrosetta.rosetta.numeric.crick_equations) single_beta_sample() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) single_ligand_motif_from_stream() (in module pyrosetta.rosetta.protocols.motifs) single_motif_from_filename() (in module pyrosetta.rosetta.protocols.motifs) single_motif_from_stream() (in module pyrosetta.rosetta.protocols.motifs) single_residue_from_stream() (in module pyrosetta.rosetta.protocols.motifs) single_state_design() (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) single_user_input_chunk() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) SingleBasicRotamerLibrary (class in pyrosetta.rosetta.core.pack.rotamers) SingleDownstreamResidueWriter (class in pyrosetta.rosetta.protocols.match.output) SingleFileBuffer (class in pyrosetta.rosetta.protocols.jd2) SingleLigandRotamerLibrary (class in pyrosetta.rosetta.core.pack.rotamers) SingleResidueCenrotLibrary (class in pyrosetta.rosetta.core.pack.dunbrack.cenrot) SingleResidueFragData (class in pyrosetta.rosetta.core.fragment) SingleResidueMultifunc (class in pyrosetta.rosetta.core.optimization) SingleResidueRotamerLibrary (class in pyrosetta.rosetta.core.pack.rotamers) SingleResidueTorsionFragmentLibrary (class in pyrosetta.rosetta.protocols.frags) SiteConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) SiteConstraintResiduesCreator (class in pyrosetta.rosetta.core.scoring.constraints) SixDCoordinateBinner (class in pyrosetta.rosetta.numeric.geometry.hashing) SixDOffsetTree (class in pyrosetta.rosetta.numeric.geometry.hashing) size() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.ConstDataMap method) (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.NoFailDataMap method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.PCluster method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) size1() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) size2() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) size_col() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) size_constraint_string() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) size_left() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) size_of_query() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) sized() (in module pyrosetta.rosetta.ObjexxFCL) skip() (in module pyrosetta.rosetta.ObjexxFCL.format) (in module pyrosetta.rosetta.utility.io) skip_chi_min() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) skip_connect_info() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) skip_coord_constraints() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) skip_minimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) skip_rate() (pyrosetta.rosetta.protocols.loops.Loop method) skip_redundant_constraints() (in module pyrosetta.rosetta.core.scoring.constraints) skip_set_reasonable_fold_tree() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) slice() (in module pyrosetta.rosetta.protocols.stepwise.modeler) slice_1base_indicies() (in module pyrosetta.bindings.utility) slice_out_pose() (in module pyrosetta.rosetta.protocols.stepwise.modeler) slice_res() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) slide_axis() (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) slide_back_to_origin() (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) slide_cutpoint() (pyrosetta.rosetta.core.kinematics.FoldTree method) slide_into_contact() (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) slide_into_contact_and_score() (in module pyrosetta.rosetta.protocols.sic_dock) slide_into_contact_and_score_DEPRICATED() (in module pyrosetta.rosetta.protocols.sic_dock) slide_jump() (in module pyrosetta.rosetta.protocols.denovo_design) (pyrosetta.rosetta.core.kinematics.FoldTree method) SlideCriteriaType (class in pyrosetta.rosetta.core.conformation.symmetry) SlideIntoContact (class in pyrosetta.rosetta.protocols.docking) SlideType (class in pyrosetta.rosetta.core.conformation.symmetry) slurp() (in module pyrosetta.rosetta.utility) SmallBBSampler (class in pyrosetta.rosetta.protocols.simple_moves.bb_sampler) smallest_ring_size() (pyrosetta.rosetta.core.chemical.ResidueType method) smallmer_from_largemer() (in module pyrosetta.rosetta.protocols.forge.methods) SmallMinCCDTrialCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) SmallMover (class in pyrosetta.rosetta.protocols.simple_moves) smooth_fa_elec() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) smooth_move_small() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) smooth_to_zero() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) SmoothEnvPairPotential (class in pyrosetta.rosetta.core.scoring) SmoothPolicy (class in pyrosetta.rosetta.protocols.nonlocal) SmoothSymmetricFragmentMover (class in pyrosetta.rosetta.protocols.simple_moves) SmotifFeaturesCreator (class in pyrosetta.rosetta.protocols.features) SnugDock (class in pyrosetta.rosetta.protocols.antibody.snugdock) SoedingFunc (class in pyrosetta.rosetta.core.scoring.func) sog_cst_param() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) SOGFunc (class in pyrosetta.rosetta.core.scoring.func) SOGFunc_Impl (class in pyrosetta.rosetta.core.scoring.func) sol_weight() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) SolutionPicker (class in pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers) solv1() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) solv2() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) solve() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) solve_gaps() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) solve_sturm() (in module pyrosetta.rosetta.numeric.kinematic_closure) SolventAccessibility (class in pyrosetta.rosetta.protocols.frag_picker.scores) solvF2BR() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) solvF2d() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) sort() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) sort_by() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) sort_by_second() (in module pyrosetta.rosetta.protocols.ligand_docking) sort_by_weighted_energy() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) sort_new_rotamers_into_rotset_vector() (in module pyrosetta.rosetta.core.pack.rotamer_set) sort_pair_list() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) sort_pose_by_score() (in module pyrosetta.rosetta.core.pose) sort_R_function() (pyrosetta.rosetta.core.optimization.EItem method) sort_residue_type_pointers_by_name() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) sort_seq_num_list() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) sort_silent_scores() (pyrosetta.rosetta.core.io.silent.SilentStruct method) sorted_res_list() (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) sorted_values() (pyrosetta.rosetta.numeric.kdtree.KDPointList method) source_chain() (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) source_file_name() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) source_filename() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) source_id_is_mapped() (pyrosetta.rosetta.utility.subset_mapping method) source_pose() (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) source_size() (pyrosetta.rosetta.utility.subset_mapping method) sources_same() (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) space() (in module pyrosetta.rosetta.ObjexxFCL) (in module pyrosetta.rosetta.ObjexxFCL.format) space_prefixed() (pyrosetta.rosetta.utility.options.OptionCollection method) SpacegroupSetting (class in pyrosetta.rosetta.protocols.cryst) spacing() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) spairs_from_foldtype() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) span_file() (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) spanfile() (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) spanfile_name() (in module pyrosetta.rosetta.core.conformation.membrane) spanfile_names() (in module pyrosetta.rosetta.core.conformation.membrane) spanning() (pyrosetta.rosetta.core.scoring.MembraneEmbed method) spanning_topology() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) spearman() (in module pyrosetta.rosetta.protocols.ligand_docking) SpecialSegmentsObserver (class in pyrosetta.rosetta.core.pose.datacache) specified_check() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) specified_report() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) sphere_lookup() (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) spheremode (class in pyrosetta.rosetta.protocols.viewer) spherical() (in module pyrosetta.rosetta.protocols.fldsgn.potentials.sspot) (pyrosetta.rosetta.core.kinematics.Stub method) spin_axis() (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) spin_id() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) spin_mag() (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) SpinAroundPartnerMoverCreator (class in pyrosetta.rosetta.protocols.membrane) spline_by_z() (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) spline_coeffs() (in module pyrosetta.rosetta.core.scoring.electron_density) spline_from_file() (in module pyrosetta.rosetta.numeric.interpolation) spline_interpolate() (in module pyrosetta.rosetta.numeric.interpolation.spline) spline_second_derivative() (in module pyrosetta.rosetta.numeric.interpolation.spline) SplineParameters (class in pyrosetta.rosetta.core.scoring.etable) split() (in module pyrosetta.rosetta.protocols.sparta) (in module pyrosetta.rosetta.utility) split_by_ca_ca_dist() (in module pyrosetta.rosetta.protocols.loops) split_by_chain() (pyrosetta.rosetta.core.pose.Pose method) split_by_newlines() (in module pyrosetta.rosetta.utility) split_by_resSeq() (in module pyrosetta.rosetta.protocols.loops) split_existing_edge_at_residue() (pyrosetta.rosetta.core.kinematics.FoldTree method) split_line_to_polyval() (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) split_line_to_spline() (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) split_mid_ranges() (in module pyrosetta.rosetta.protocols.fold_from_loops.utils) split_pose() (in module pyrosetta.rosetta.protocols.stepwise.modeler) split_sequence_motif() (in module pyrosetta.rosetta.core.sequence) split_to_list() (in module pyrosetta.rosetta.utility) split_to_set() (in module pyrosetta.rosetta.utility) split_topology_by_jump() (in module pyrosetta.rosetta.protocols.membrane) split_topology_by_jump_noshift() (in module pyrosetta.rosetta.protocols.membrane) split_unfolded_label_type() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) split_unfolded_value_type() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) split_up_remark_line() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) split_WhiteSpace() (in module pyrosetta.rosetta.protocols.sparta) split_whitespace() (in module pyrosetta.rosetta.utility) SplitAndMixPoseMoverCreator (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) sq_vec_distance() (in module pyrosetta.rosetta.numeric.kdtree) sqr() (in module pyrosetta.rosetta.numeric.interpolation.spline) square() (in module pyrosetta.rosetta.ObjexxFCL) square_distance() (pyrosetta.rosetta.core.scoring.EnergyEdge method) src_pose() (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) src_pose_start() (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) SS() (in module pyrosetta.rosetta.ObjexxFCL.format) ss() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) ss_element_id() (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) ss_index() (in module pyrosetta.rosetta.protocols.frag_picker.quota) SS_Info (class in pyrosetta.rosetta.core.scoring) SS_Info2 (class in pyrosetta.rosetta.protocols.fldsgn.topology) SS_Killhairpins_Info (class in pyrosetta.rosetta.core.scoring) ss_length_check() (in module pyrosetta.rosetta.protocols.frags) ss_penalty() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) ss_str() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) ssbond_map() (pyrosetta.rosetta.core.io.StructFileRep method) SSBondInformation (class in pyrosetta.rosetta.core.io) SSElementSelector (class in pyrosetta.rosetta.core.select.residue_selector) SSManager (class in pyrosetta.rosetta.core.sequence) SSPairPotential (class in pyrosetta.rosetta.protocols.fldsgn.potentials.sspot) SSType (class in pyrosetta.rosetta.protocols.comparative_modeling.features) st_atr() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) st_rep() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) st_sol() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) stage1_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) stage2_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) stage3_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) stage4_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) stage5_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) StageID (class in pyrosetta.rosetta.protocols.abinitio) (class in pyrosetta.rosetta.protocols.abinitio.abscript) standard_RG (class in pyrosetta.rosetta.numeric.random) StandardDisulfPairingLibrary (class in pyrosetta.rosetta.protocols.jumping) StandardJobQueen (class in pyrosetta.rosetta.protocols.jd3.standard) StandardPairingLibrary (class in pyrosetta.rosetta.protocols.jumping) StandardPivots (class in pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers) Star (class in pyrosetta.rosetta.ObjexxFCL) star_fold_tree() (in module pyrosetta.rosetta.protocols.protein_interface_design) StarAbinitio_main() (in module pyrosetta.rosetta.protocols.star) start() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.jumping.Interval method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.nonlocal.Chunk method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) start_atom() (pyrosetta.rosetta.core.kinematics.Edge method) start_atomid() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) start_atomid1() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) start_atomid2() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) start_atoms1() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) start_atoms2() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) start_doc() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) start_evaluation_timer() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) start_file() (in module pyrosetta.rosetta.basic.options) start_files() (in module pyrosetta.rosetta.basic.options) start_from_centroid() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) start_key() (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) start_list() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) start_local() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) start_map() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) start_new_batch() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) start_res() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation method) start_seq2() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) start_time() (pyrosetta.rosetta.protocols.jd2.Job method) start_timing() (pyrosetta.rosetta.protocols.jd2.Job method) start_tree_at_chain() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) starting_node() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) starting_pose() (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) startswith() (in module pyrosetta.rosetta.utility) startup() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) state() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) state_momento() (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) state_unassigned() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) states() (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) StaticIndexRange (class in pyrosetta.rosetta.ObjexxFCL) statistics_valid() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) StatsType (class in pyrosetta.rosetta.protocols.moves) status() (pyrosetta.rosetta.protocols.jd3.JobResult method) status_prefix() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) status_suffix() (pyrosetta.rosetta.protocols.jd3.LarvalJob method) steal() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) steal_alignment() (in module pyrosetta.rosetta.core.sequence) steal_constant_length_frag_set_from_pose() (in module pyrosetta.rosetta.core.fragment) steal_def() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) steal_def_clone() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) steal_frag_set_from_pose() (in module pyrosetta.rosetta.core.fragment) steal_inversion() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) steal_ligands() (in module pyrosetta.rosetta.protocols.comparative_modeling) steepness() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) step() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) step_count() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) step_size() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) stepsize() (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) stepwise_addable_pose_residue() (in module pyrosetta.rosetta.core.pose) stepwise_addable_residue() (in module pyrosetta.rosetta.core.pose) StepWiseLegacyClusterer (class in pyrosetta.rosetta.protocols.stepwise.modeler.align) StepWiseLegacyClustererSilentBased (class in pyrosetta.rosetta.protocols.stepwise.modeler.align) StepWiseModelerOptions (class in pyrosetta.rosetta.protocols.stepwise.modeler.options) StepWiseMove (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) StepWisePacker (class in pyrosetta.rosetta.protocols.stepwise.modeler.packer) StepWiseProteinBackboneSampler (class in pyrosetta.rosetta.protocols.stepwise.modeler.protein) StepWiseProteinCCD_Closer (class in pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close) StepWiseProteinKIC_LoopBridger (class in pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close) StepWiseProteinMinimizer (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) StepWiseProteinPoseSetup (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) StepWiseRNA_Clusterer (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) StepWiseRNA_PoseSetup (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) StepWiseScreenerType (class in pyrosetta.rosetta.protocols.stepwise.screener) StepWiseWorkingParametersSetup (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) still_interested() (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) stop() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.jumping.Interval method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.nonlocal.Chunk method) stop_at_closure() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) stop_atom() (pyrosetta.rosetta.core.kinematics.Edge method) stop_local() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) stop_res() (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) stop_sampling() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) stopping_condition() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) store_active_energies() (pyrosetta.rosetta.core.scoring.EnergyEdge method) store_argv_in_file() (pyrosetta.rosetta.core.io.silent.SilentFileData method) store_base_residue_type_name_in_sfr() (in module pyrosetta.rosetta.core.io.pdb) store_classification() (pyrosetta.rosetta.core.io.HeaderInformation method) store_compound() (pyrosetta.rosetta.core.io.HeaderInformation method) store_connection_architect() (in module pyrosetta.rosetta.protocols.denovo_design.connection) store_constraints() (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) store_CSA_in_pose() (in module pyrosetta.rosetta.core.scoring) store_current_derivatives() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) store_DC_in_pose() (in module pyrosetta.rosetta.core.scoring) store_denovo_architect() (in module pyrosetta.rosetta.protocols.denovo_design.architects) store_deposition_date() (pyrosetta.rosetta.core.io.HeaderInformation method) store_experimental_technique() (pyrosetta.rosetta.core.io.HeaderInformation method) store_experimental_techniques() (pyrosetta.rosetta.core.io.HeaderInformation method) store_H3_cter_fragment() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) store_idCode() (pyrosetta.rosetta.core.io.HeaderInformation method) store_keywords() (pyrosetta.rosetta.core.io.HeaderInformation method) store_line() (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) store_new_sphere() (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) store_RDC_in_pose() (in module pyrosetta.rosetta.core.scoring) store_RDC_ROHL_in_pose() (in module pyrosetta.rosetta.core.scoring) store_RDC_segments_in_pose() (in module pyrosetta.rosetta.protocols.scoring) store_title() (pyrosetta.rosetta.core.io.HeaderInformation method) store_trie() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) store_xyz() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) StoreCombinedStoredTasksMover (class in pyrosetta.rosetta.protocols.task_operations) stored_data() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) stored_induced_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) stored_induced_rf_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) StoredResidueSubsetSelector (class in pyrosetta.rosetta.protocols.residue_selectors) StoredRotamerLibrarySpecification (class in pyrosetta.rosetta.core.chemical.rotamers) StorePoseSnapshot (class in pyrosetta.rosetta.protocols.simple_moves) StoreResidueSubsetMover (class in pyrosetta.rosetta.protocols.residue_selectors) stores_residue_map() (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) StoreTaskMover (class in pyrosetta.rosetta.protocols.task_operations) str() (pyrosetta.rosetta.basic.datacache.CacheableString method) str_dn() (in module pyrosetta.rosetta.ObjexxFCL) str_dncase() (in module pyrosetta.rosetta.ObjexxFCL) str_up() (in module pyrosetta.rosetta.ObjexxFCL) str_upcase() (in module pyrosetta.rosetta.ObjexxFCL) Strand (class in pyrosetta.rosetta.protocols.fldsgn.topology) strand() (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) strand_fraction() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) strand_id() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) strand_id1() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) strand_id2() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) strand_pairing() (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) strand_pairing_set() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) strand_pairings() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) StrandArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) StrandBundleFeaturesCreator (class in pyrosetta.rosetta.protocols.features.strand_assembly) StrandCurvatureByLevels (class in pyrosetta.rosetta.protocols.fldsgn.filters) StrandHelixGeometryFilter (class in pyrosetta.rosetta.protocols.fldsgn.filters) StrandOrientation (class in pyrosetta.rosetta.protocols.denovo_design.components) StrandPairing (class in pyrosetta.rosetta.core.scoring.dssp) StrandPairingSet (class in pyrosetta.rosetta.core.scoring.dssp) (class in pyrosetta.rosetta.protocols.fldsgn.topology) Strands (class in pyrosetta.rosetta.core.scoring) strands() (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) StrandTwistingMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) Strategy (class in pyrosetta.rosetta.core.conformation) strategy() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) stream() (pyrosetta.rosetta.basic.resource_manager.locator.FileStream method) (pyrosetta.rosetta.basic.resource_manager.ResourceStream method) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream method) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) streams_from_cmd_line() (in module pyrosetta.rosetta.core.import_pose.pose_stream) strict_column_mode() (pyrosetta.rosetta.core.io.silent.SilentFileData method) strict_looprelax_checks() (pyrosetta.rosetta.protocols.loops.Loops method) strict_lower() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) strict_upper() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) stride() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) string2float() (in module pyrosetta.rosetta.utility) string2int() (in module pyrosetta.rosetta.utility) string2Real() (in module pyrosetta.rosetta.utility) string2Size() (in module pyrosetta.rosetta.utility) string2uint() (in module pyrosetta.rosetta.utility) string_blosum() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) string_contains_gt_lt_or_ampersand() (in module pyrosetta.rosetta.utility.tag) string_from_property() (pyrosetta.rosetta.core.chemical.AtomPropertiesManager method) string_from_type_set_mode() (in module pyrosetta.rosetta.core.chemical) string_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) string_path() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) string_properties() (pyrosetta.rosetta.core.chemical.ResidueProperties method) string_rep() (pyrosetta.rosetta.protocols.contact_map.Contact method) (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) string_split() (in module pyrosetta.rosetta.utility) string_split_multi_delim() (in module pyrosetta.rosetta.utility) string_split_simple() (in module pyrosetta.rosetta.utility) string_to_compound_token() (pyrosetta.rosetta.core.io.HeaderInformation method) string_to_experimental_technique() (pyrosetta.rosetta.core.io.HeaderInformation method) string_to_hb_eval_type() (in module pyrosetta.rosetta.core.scoring.hbonds) string_to_int() (in module pyrosetta.rosetta.core.pose.rna) (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) string_to_real() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) string_to_sha1() (in module pyrosetta.rosetta.utility) string_value() (pyrosetta.rosetta.core.io.silent.SilentEnergy method) stringafteroption() (in module pyrosetta.rosetta.basic.options) StringMetric (class in pyrosetta.rosetta.core.simple_metrics) StringOption (class in pyrosetta.rosetta.utility.options) StringOptionKey (class in pyrosetta.rosetta.utility.options) StringResourceStream (class in pyrosetta.rosetta.basic.resource_manager.locator) StringVectorOption (class in pyrosetta.rosetta.utility.options) StringVectorOptionKey (class in pyrosetta.rosetta.utility.options) strip() (in module pyrosetta.rosetta.ObjexxFCL) (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) strip_out_magnesiums() (in module pyrosetta.rosetta.protocols.magnesium) strip_rotamer_library_specification() (pyrosetta.rosetta.core.chemical.ResidueType method) strip_spacers() (in module pyrosetta.rosetta.core.sequence) strip_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) stripped() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) stripped_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) StrongWolfe() (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) StrongWolfeLineMinimization (class in pyrosetta.rosetta.core.optimization) struct_from_job() (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) struct_ids_from_tag() (in module pyrosetta.rosetta.protocols.features) StructFileRep (class in pyrosetta.rosetta.core.io) StructFragmentMoverCreator (class in pyrosetta.rosetta.protocols.struct_fragment) structure_has_moved() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) structure_list() (pyrosetta.rosetta.core.io.silent.SilentFileData method) structure_moved() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) StructureArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) StructureDataFactory (class in pyrosetta.rosetta.protocols.denovo_design.components) StructureDataObserver (class in pyrosetta.rosetta.protocols.denovo_design.components) StructureDataPerturber (class in pyrosetta.rosetta.protocols.denovo_design.components) StructureFeaturesCreator (class in pyrosetta.rosetta.protocols.features) StructureScoresFeaturesCreator (class in pyrosetta.rosetta.protocols.features) StructureSimilarityEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) Stub (class in pyrosetta.rosetta.core.kinematics) stub_atom() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) stub_atom1() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) stub_atom1_id() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) stub_atom2() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) stub_atom2_id() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) stub_atom3() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) stub_atom3_id() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) stub_defined() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) stub_from_id() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.pose.Pose method) stub_from_points() (in module pyrosetta.rosetta.protocols.hotspot_hashing) stub_id_to_named_stub_id() (in module pyrosetta.rosetta.core.conformation) (in module pyrosetta.rosetta.core.pose) stub_minimize_movers() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) stub_sets() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) stub_tgt_angle() (in module pyrosetta.rosetta.protocols.hotspot_hashing) stub_to_points() (in module pyrosetta.rosetta.protocols.hotspot_hashing) StubID (class in pyrosetta.rosetta.core.id) StubMode (class in pyrosetta.rosetta.protocols.cyclic_peptide) StubStatus (class in pyrosetta.rosetta.protocols.hotspot_hashing) StubStubType (class in pyrosetta.rosetta.core.pose.rna) sub_rank() (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) sub_to_full() (in module pyrosetta.rosetta.core.pose.full_model_info) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) subdir() (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepSequence method) subelement_behavior() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) subelement_ct_namer() (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) submotif_info() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) submotif_info_containing_residues() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) submotif_info_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) submotif_library() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) submotif_tag() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) SubMotifInfo (class in pyrosetta.rosetta.core.pose.full_model_info) submover() (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) subset() (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) subset_mapping (class in pyrosetta.rosetta.utility) substate() (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) substitute_residue() (in module pyrosetta.rosetta.protocols.dna) substitution_group() (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) subtract_chi_angles() (in module pyrosetta.rosetta.core.pack.dunbrack) subtract_degree_angles() (in module pyrosetta.rosetta.basic) subtract_radian_angles() (in module pyrosetta.rosetta.basic) success() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) suffix() (pyrosetta.rosetta.utility.options.OptionCollection method) suffix_from_jd_with_sep() (pyrosetta.rosetta.protocols.jd3.output.OutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification method) sugar_modifications_from_suffix() (in module pyrosetta.rosetta.core.io.carbohydrates) SugarBackboneEnergy (class in pyrosetta.rosetta.core.scoring.methods.carbohydrates) SugarBackboneEnergyCreator (class in pyrosetta.rosetta.core.scoring.methods.carbohydrates) SugarBBSampler (class in pyrosetta.rosetta.protocols.simple_moves.bb_sampler) SugarModificationsNomenclatureTableRow (class in pyrosetta.rosetta.core.chemical.carbohydrates) suggest_residue_number() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) suite_rmsd() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) suite_square_deviation() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) sum() (pyrosetta.rosetta.core.scoring.EMapVector method) sum_constraint_scoreterms() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) sum_energies() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) sum_total_residue_energy() (in module pyrosetta.rosetta.protocols.protein_interface_design) super_mute() (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerImpl method) super_twiddles() (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) superimpose_all() (in module pyrosetta.rosetta.protocols.mpi_refinement) superimpose_overhangs_heavy() (in module pyrosetta.rosetta.protocols.grafting) superimpose_pose() (in module pyrosetta.rosetta.core.scoring) superimpose_pose_legacy() (in module pyrosetta.rosetta.protocols.stepwise.modeler.align) superimpose_pose_on_subset_bb() (in module pyrosetta.rosetta.protocols.fibril) superimpose_pose_on_subset_CA() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) superimpose_to_single_user_input_chunk() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) superimpose_with_stepwise_aligner() (in module pyrosetta.rosetta.protocols.stepwise.modeler.align) SuperimposeMover (class in pyrosetta.rosetta.protocols.simple_moves) superposition_transform() (in module pyrosetta.rosetta.protocols.seeded_abinitio) (in module pyrosetta.rosetta.protocols.toolbox) suppress_CSI_codes() (pyrosetta.rosetta.utility.CSI_Sequence method) suppress_zero_occ_pdb_output() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) surface_exposed_nb_cutoff() (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation method) SurfaceEnergies (class in pyrosetta.rosetta.core.scoring.solid_surface) SurfaceEnergy (class in pyrosetta.rosetta.core.pack.interaction_graph) SurfacePotential (class in pyrosetta.rosetta.core.pack.interaction_graph) SurfaceVectorLoader (class in pyrosetta.rosetta.protocols.surface_docking) SurrogateVariableExpression (class in pyrosetta.rosetta.protocols.pack_daemon) svdcmp() (in module pyrosetta.rosetta.numeric.linear_algebra) SW() (in module pyrosetta.rosetta.ObjexxFCL.format) swap() (in module pyrosetta.rosetta.ObjexxFCL) (in module pyrosetta.rosetta.std) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) swap4_aligned() (in module pyrosetta.rosetta.utility) swap_coordinates_in_pose() (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) swap_in() (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) swap_in_movemap() (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) swap_no_notify() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) swap_transform() (in module pyrosetta.rosetta.core.pose) sweep_incomplete() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) switch_conformer() (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) switch_focus_among_poses_randomly() (in module pyrosetta.rosetta.protocols.stepwise.modeler) switch_focus_to_other_pose() (in module pyrosetta.rosetta.protocols.stepwise.modeler) switch_movemap() (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.Loops method) switch_residue_type_set() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) switch_to_centroid_rot_set() (in module pyrosetta.rosetta.core.util) switch_to_fullatom() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) switch_to_residue_type_set() (in module pyrosetta.rosetta.core.util) SwitchMover (class in pyrosetta.rosetta.protocols.moves) SwitchResidueTypeSetMover (class in pyrosetta.rosetta.protocols.simple_moves) sym_dof_jump_num() (in module pyrosetta.rosetta.core.pose.symmetry) sym_dof_name() (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) sym_dof_names() (in module pyrosetta.rosetta.core.pose.symmetry) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) SymAtomTreeMinimizer (class in pyrosetta.rosetta.core.optimization.symmetry) SymAtomTreeMultifunc (class in pyrosetta.rosetta.core.optimization.symmetry) symbol2index() (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.core.sequence.SSManager method) symbolString2base5index() (pyrosetta.rosetta.core.sequence.ABEGOManager method) symbolString2index() (pyrosetta.rosetta.core.sequence.SSManager method) SymDock_main() (in module pyrosetta.rosetta.protocols.symmetric_docking) SymDockingSlideIntoContact (class in pyrosetta.rosetta.protocols.symmetry) SymDockProtocol (class in pyrosetta.rosetta.protocols.symmetric_docking) SymDofMover (class in pyrosetta.rosetta.protocols.matdes) SymDofMoverSampler (class in pyrosetta.rosetta.protocols.matdes) SymEnergyCutRotamerTrialsMover (class in pyrosetta.rosetta.protocols.minimization_packing.symmetry) SymFoldandDockMoveRbJumpMover (class in pyrosetta.rosetta.protocols.symmetric_docking) SymFoldandDockSlideTrialMover (class in pyrosetta.rosetta.protocols.symmetric_docking) symm_count() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) symm_repeats() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) symm_type() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) symmetric_components() (in module pyrosetta.rosetta.core.pose.symmetry) symmetric_fold_tree() (in module pyrosetta.rosetta.protocols.denovo_design) symmetric_gly_tables() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) symmetric_residue_subset() (in module pyrosetta.rosetta.protocols.denovo_design) symmetric_rotamer_trials() (in module pyrosetta.rosetta.core.pack) symmetric_secstruct() (in module pyrosetta.rosetta.protocols.denovo_design) symmetric_sequence() (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) SymmetricAddMembraneMoverCreator (class in pyrosetta.rosetta.protocols.membrane.symmetry) SymmetricalResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) SymmetricConformation (class in pyrosetta.rosetta.core.conformation.symmetry) SymmetricCycpepAlign (class in pyrosetta.rosetta.protocols.cyclic_peptide) SymmetricFragmentMover (class in pyrosetta.rosetta.protocols.simple_moves) SymmetricRMSMover (class in pyrosetta.rosetta.protocols.symmetry) SymmetricRotamerSet_ (class in pyrosetta.rosetta.core.pack.rotamer_set.symmetry) symmetrize_by_intersection() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) symmetrize_by_union() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) symmetrize_fold_tree() (in module pyrosetta.rosetta.core.conformation.symmetry) (in module pyrosetta.rosetta.core.pose.symmetry) symmetrize_scorefunction() (in module pyrosetta.rosetta.core.scoring.symmetry) symmetrize_spans() (in module pyrosetta.rosetta.protocols.membrane.symmetry) symmetry_compliance() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) symmetry_info() (in module pyrosetta.rosetta.core.pose.symmetry) Symmetry_Info() (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) symmetry_repeats() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) SymMinimizeInterface() (in module pyrosetta.rosetta.protocols.protein_interface_design) SymMinimizerMap (class in pyrosetta.rosetta.core.optimization.symmetry) SymMinMover (class in pyrosetta.rosetta.protocols.minimization_packing.symmetry) SymPackRotamersMover (class in pyrosetta.rosetta.protocols.minimization_packing.symmetry) SymRotamerTrialsMover (class in pyrosetta.rosetta.protocols.minimization_packing.symmetry) SymUnsatHbondFilter (class in pyrosetta.rosetta.protocols.matdes) SYN_ANTI_RESTRICTION (class in pyrosetta.rosetta.core.fragment.rna) sync_objects_with_flags() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) sys_sleep() (in module pyrosetta.rosetta.utility)

T

T (class in pyrosetta.rosetta.protocols.features.RelevantResiduesMode) t_str() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) tab_prefixed() (pyrosetta.rosetta.utility.options.OptionCollection method) table_exists() (in module pyrosetta.rosetta.basic.database) TabooSamplingKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) tabulate() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) tag() (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepSequence method) (pyrosetta.rosetta.core.import_pose.libraries.BasePairType method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) tag_from_line() (in module pyrosetta.rosetta.core.chemical) tag_from_pdb_fname() (in module pyrosetta.rosetta.core.scoring.motif) tag_from_pose() (in module pyrosetta.rosetta.core.pose) tag_into_pose() (in module pyrosetta.rosetta.core.pose) tag_time() (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) tags() (pyrosetta.rosetta.core.io.silent.SilentFileData method) tail() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) TailFunction (class in pyrosetta.rosetta.core.scoring.aa_composition_energy) (class in pyrosetta.rosetta.core.scoring.netcharge_energy) take_coordinates_from_pose() (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) takeoff_domain() (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) takeoff_pos() (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) TalosSSSimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) targ_ang() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) targ_dih() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) TARGET (class in pyrosetta.rosetta.core.pack.task) target() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) target_chain() (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) target_pose_start() (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) target_res() (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) target_res_for_geom_cst() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) target_residues() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) target_seq() (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) target_sequence() (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation method) target_type() (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) TargetPocketGrid (class in pyrosetta.rosetta.protocols.pockets) targetPocketHeuristicScore() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) targetPocketHydrophobicProteinSurface() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) targetPocketPolarProteinSurface() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) targetPocketProteinSurface() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) targetPocketSolventSurface() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) targetPocketVolume() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) task() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) task_factory() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) task_initialized() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) task_is_valid() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) task_op_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.TaskOperationLoader method) task_op_schema_empty() (in module pyrosetta.rosetta.core.pack.task.operation) task_op_schema_w_attributes() (in module pyrosetta.rosetta.core.pack.task.operation) task_scaling() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) task_string() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) TaskAwareCsts (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) TaskAwareMinMover (class in pyrosetta.rosetta.protocols.minimization_packing) TaskFactory (class in pyrosetta.rosetta.core.pack.task) TaskOperationCreator (class in pyrosetta.rosetta.core.pack.task.operation) TaskOperationFeaturesCreator (class in pyrosetta.rosetta.protocols.features) TaskOperationLoader (class in pyrosetta.rosetta.protocols.parser) TaskOperationMPM (class in pyrosetta.rosetta.protocols.match) tasks() (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) TaskSelector (class in pyrosetta.rosetta.protocols.residue_selectors) TBMB_Helper (class in pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) temp() (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) temp1() (pyrosetta.rosetta.core.scoring.AtomNeighbor method) temp2() (pyrosetta.rosetta.core.scoring.AtomNeighbor method) temp3() (pyrosetta.rosetta.core.scoring.AtomNeighbor method) temp4() (pyrosetta.rosetta.core.scoring.AtomNeighbor method) temp_file() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) temperature() (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) temperature_level() (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) temperature_move() (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) TemperatureController (class in pyrosetta.rosetta.protocols.canonical_sampling) temperatures() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) TemperedDocking (class in pyrosetta.rosetta.protocols.docking) tempering() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) TemperingBase (class in pyrosetta.rosetta.protocols.canonical_sampling) template_file() (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) template_name() (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation method) template_pose() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) TemplateFragmentClaimer (class in pyrosetta.rosetta.protocols.topology_broker) TemplateHistory (class in pyrosetta.rosetta.protocols.hybridization) TemplateJumpClaimer (class in pyrosetta.rosetta.protocols.topology_broker) templates_from_cmd_line() (in module pyrosetta.rosetta.protocols.comparative_modeling) temporarily_fix_everything() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) temporarily_set_pack_residue() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) temps() (pyrosetta.rosetta.core.io.ResidueInformation method) tenA_neighbor_graph() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) tensor() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) terCount() (pyrosetta.rosetta.core.io.ResidueInformation method) termini_penalty() (pyrosetta.rosetta.core.scoring.MembranePotential method) TerminiConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) Terminus (class in pyrosetta.rosetta.core.pose.rna) test_all_mg_hydration_frames() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) test_chunk() (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter method) test_if_schema_is_valid() (in module pyrosetta.rosetta.utility.tag) test_move() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) test_res_res_aln() (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) testNeighbor() (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.PCluster method) TestStringMetric (class in pyrosetta.rosetta.core.simple_metrics) tether_jump() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) TheozymeInvrotTree (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) thermal_sampler_output_min_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) thermal_sampler_temperature() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) ThermalMinimizer (class in pyrosetta.rosetta.protocols.recces.scratch) ThermalSamplingMover (class in pyrosetta.rosetta.protocols.recces.scratch) ThermodynamicData (class in pyrosetta.rosetta.protocols.simple_moves) ThermodynamicMover (class in pyrosetta.rosetta.protocols.canonical_sampling) ThermodynamicObserver (class in pyrosetta.rosetta.protocols.canonical_sampling) theta() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.pose.Pose method) thickness() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) thread_sequence_on_pose() (in module pyrosetta.rosetta.protocols.evolution.AlignmentCleanerTools) ThreadingJob (class in pyrosetta.rosetta.protocols.comparative_modeling) ThreadingJobInputter (class in pyrosetta.rosetta.protocols.comparative_modeling) ThreadSequenceOperation (class in pyrosetta.rosetta.protocols.task_operations) threshold() (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) tighten_memory() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.pose.PDBInfo method) tilt1_center() (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) tilt1_mag() (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) tilt2_center() (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) tilt2_mag() (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) TiltMover (class in pyrosetta.rosetta.protocols.membrane) TiltMoverCreator (class in pyrosetta.rosetta.protocols.membrane) time_to_checkpoint() (pyrosetta.rosetta.protocols.checkpoint.Timer method) Timer (class in pyrosetta.rosetta.protocols.checkpoint) timestamp() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.protocols.jd2.Job method) timestamp_millis() (in module pyrosetta.rosetta.utility) timestamp_millis_short() (in module pyrosetta.rosetta.utility) timestamp_short() (in module pyrosetta.rosetta.utility) TimingProfileMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) title() (pyrosetta.rosetta.core.io.HeaderInformation method) title_width() (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) tm_projection_penalty() (pyrosetta.rosetta.core.scoring.MembranePotential method) TMA_Helper (class in pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) tmpbuf() (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) TMscoreStore (class in pyrosetta.rosetta.core.scoring) to_all_atom() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) to_bare_name() (pyrosetta.rosetta.utility.file.FileName method) to_centroid() (in module pyrosetta.rosetta.protocols.medal) (in module pyrosetta.rosetta.protocols.star) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) to_default() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) to_degrees() (in module pyrosetta.rosetta.numeric.conversions) (in module pyrosetta.rosetta.numeric.kinematic_closure.radians) to_do() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) to_left() (in module pyrosetta.rosetta.core.membrane) to_local_name() (pyrosetta.rosetta.utility.file.FileName method) to_multichain_pose() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) to_pose() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) to_radians() (in module pyrosetta.rosetta.numeric.kinematic_closure.radians) to_string() (in module pyrosetta.rosetta.core.id) (in module pyrosetta.rosetta.core.pose.full_model_info) (in module pyrosetta.rosetta.core.scoring.rna) (in module pyrosetta.rosetta.numeric.interpolation) (in module pyrosetta.rosetta.protocols.moves) (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) toFloat() (in module pyrosetta.rosetta.protocols.cluster.calibur) toInt() (in module pyrosetta.rosetta.protocols.cluster.calibur) token_type_name() (in module pyrosetta.rosetta.numeric.expression_parser) tokenize() (in module pyrosetta.rosetta.core.pose.rna) (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) tokenize_line() (in module pyrosetta.rosetta.core.pack.task) TokenType (class in pyrosetta.rosetta.numeric.expression_parser) tolerance() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) tolerated_overlap() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) ToolboxKeys (class in pyrosetta.rosetta.protocols.loop_modeling) top_fragments() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) TopNByProperty (class in pyrosetta.rosetta.protocols.pose_selectors) topological_match_to() (pyrosetta.rosetta.core.kinematics.AtomTree method) topological_observers() (pyrosetta.rosetta.core.kinematics.AtomTree method) topological_sort() (in module pyrosetta.rosetta.utility.graph) topology_broker() (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) TopologyBrokerMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) TopologyClaimerFactory (class in pyrosetta.rosetta.protocols.topology_broker) tor_U1D3_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) tor_U2D2_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) tor_U3D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) torsion() (in module pyrosetta.rosetta.numeric.kinematic_closure) (in module pyrosetta.rosetta.numeric.kinematic_closure.radians) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.pose.Pose method) torsion2big_bin() (in module pyrosetta.rosetta.protocols.frags) torsion2big_bin_id() (in module pyrosetta.rosetta.protocols.frag_picker.quota) torsion2index() (pyrosetta.rosetta.core.sequence.ABEGOManager method) torsion2index_level1() (pyrosetta.rosetta.core.sequence.ABEGOManager method) torsion2index_level2() (pyrosetta.rosetta.core.sequence.ABEGOManager method) torsion2index_level3() (pyrosetta.rosetta.core.sequence.ABEGOManager method) torsion2index_level4() (pyrosetta.rosetta.core.sequence.ABEGOManager method) torsion_angle() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) torsion_angle_dof_id() (pyrosetta.rosetta.core.kinematics.AtomTree method) torsion_constraints_from_chi_rotamers() (in module pyrosetta.rosetta.protocols.ligand_docking) torsion_constraints_from_rotamers() (in module pyrosetta.rosetta.protocols.ligand_docking) torsion_ct_name() (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) torsion_delta() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) torsion_features_string() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) torsion_id() (pyrosetta.rosetta.core.id.TorsionID_Range method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) torsion_id_begin() (pyrosetta.rosetta.core.kinematics.MoveMap method) torsion_id_end() (pyrosetta.rosetta.core.kinematics.MoveMap method) torsion_id_ranges() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method)

Torsion_Info (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna) torsion_name() (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) torsion_sample_value() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) torsion_scale_factor() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) torsion_type_begin() (pyrosetta.rosetta.core.kinematics.MoveMap method) torsion_type_end() (pyrosetta.rosetta.core.kinematics.MoveMap method) torsional_derivative_from_cartesian_derivatives() (in module pyrosetta.rosetta.core.optimization) TorsionBin (class in pyrosetta.rosetta.protocols.comparative_modeling.features) TorsionBinSimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) TorsionDOFMover (class in pyrosetta.rosetta.protocols.simple_moves) TorsionFragment (class in pyrosetta.rosetta.protocols.frags) TorsionFragmentLibrary (class in pyrosetta.rosetta.protocols.frags) TorsionID (class in pyrosetta.rosetta.core.id) TorsionID_Range (class in pyrosetta.rosetta.core.id) TorsionPerturbType (class in pyrosetta.rosetta.protocols.simple_moves) TorsionRestrictedKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) torsions() (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) TorsionSamplingKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) TorsionSweepingKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) TorsionType (class in pyrosetta.rosetta.core.id) total_accepts() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) total_atoms() (pyrosetta.rosetta.core.pose.Pose method) total_buried_volume() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) total_counts() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) total_energies() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) total_energy() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) total_energy_from_pose() (in module pyrosetta.rosetta.core.pose) total_nr_jobs() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) total_number_abego() (pyrosetta.rosetta.core.sequence.ABEGOManager method) total_proposed() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) total_residue() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.SameStrand method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) total_score() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) total_score_of_last_considered_pose() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) total_size() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) total_standard_cycles() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) total_trials() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) TotalEnergyMetric (class in pyrosetta.rosetta.protocols.analysis.simple_metrics) Tracer (class in pyrosetta.rosetta.basic) TracerImpl (class in pyrosetta.rosetta.basic) TracerOptions (class in pyrosetta.rosetta.basic) TracerPriority (class in pyrosetta.rosetta.basic) traits() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) traits_string() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) TrajectoryLogger (class in pyrosetta.rosetta.protocols.loop_modeling.utilities) TrajectoryMapFeaturesCreator (class in pyrosetta.rosetta.protocols.features) TrajectoryRecorder (class in pyrosetta.rosetta.protocols.canonical_sampling) TrajectoryState (class in pyrosetta.rosetta.protocols.viewer.graphics_states_param) trans_axis() (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) trans_magnitude() (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) trans_omega() (in module pyrosetta.rosetta.protocols.forge.methods) trans_pose() (in module pyrosetta.rosetta.protocols.sic_dock) transaction_mode_from_name() (in module pyrosetta.rosetta.utility.sql_database) transfer_constraint_set() (pyrosetta.rosetta.core.pose.Pose method) transfer_jumps() (in module pyrosetta.rosetta.core.pose) transfer_phi_psi() (in module pyrosetta.rosetta.core.pose) transform() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) transform_Ax_plus_b_recursive() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) transform_model() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) transform_moving_partition_to_origin() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) transform_percentile() (in module pyrosetta.rosetta.numeric.kdtree) transform_percentile_single_pt() (in module pyrosetta.rosetta.numeric.kdtree) transform_res_to_subunit() (in module pyrosetta.rosetta.protocols.loop_grower) transform_to_closest_symmunit() (in module pyrosetta.rosetta.protocols.loop_grower) TransformIntoMembraneMover (class in pyrosetta.rosetta.protocols.membrane) TransformIntoMembraneMoverCreator (class in pyrosetta.rosetta.protocols.membrane) transforms_uptodate() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) transitive_map() (in module pyrosetta.rosetta.core.sequence) translate() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) translate_and_rotate_residue_to_origin() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) translate_by() (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) translate_pose() (in module pyrosetta.toolbox.numpy_utils) translate_virtual_anchor_to_first_rigid_body() (in module pyrosetta.rosetta.protocols.rna.denovo) translation() (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) translation_along_axis() (pyrosetta.rosetta.core.kinematics.Jump method) TranslationFreePeptideMover (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers) TranslationMover (class in pyrosetta.rosetta.protocols.membrane) TranslationMoverCreator (class in pyrosetta.rosetta.protocols.membrane) TranslationRotationMover (class in pyrosetta.rosetta.protocols.membrane) TranslationRotationMoverCreator (class in pyrosetta.rosetta.protocols.membrane) transpose_product() (in module pyrosetta.rosetta.numeric) transpose_so3() (in module pyrosetta.rosetta.numeric.fourier) tree_from_jumps_and_cuts() (pyrosetta.rosetta.core.kinematics.FoldTree method) tree_init() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) trial_counter() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) TrialCounterObserver (class in pyrosetta.rosetta.protocols.canonical_sampling) TrialCounterObserverCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) TrialMover (class in pyrosetta.rosetta.protocols.moves) TrialResult (class in pyrosetta.rosetta.protocols.monte_carlo) tries() (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) trigger_accept() (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) trim() (in module pyrosetta.rosetta.ObjexxFCL) (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.utility.options.OptionCollection method) trim_back_sequence_mapping() (in module pyrosetta.rosetta.protocols.loops) trim_framework() (in module pyrosetta.rosetta.protocols.antibody.grafting) trim_neighbors_by_distance() (in module pyrosetta.rosetta.core.select) trim_scores() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) trim_to_single_repeat() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) trim_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) trimmed() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.utility.options.OptionCollection method) trimmed_compare() (in module pyrosetta.rosetta.utility) trimmed_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) trimmed_whitespace_range() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) truefalseoption() (in module pyrosetta.rosetta.basic.options) truncate_abego() (in module pyrosetta.rosetta.protocols.denovo_design.components) trust() (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) trust_fold_tree() (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) trytry_ifstream_open() (in module pyrosetta.rosetta.utility.file) trytry_ofstream_open() (in module pyrosetta.rosetta.utility.file) turn_off_cter_insert() (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) turn_off_H3_filter() (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) turn_off_rna_chem_map_during_optimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) twelveA_neighbor_graph() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) twist_level() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) two_parts_chain1() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) two_step() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) twoprime_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) type() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.conformation.Atom method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.TotalEnergyMetric method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaType method) type_for_fake_atoms() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) type_name() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator method) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator method) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator method) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalRequirementCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaType method) type_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) type_ptr() (pyrosetta.rosetta.core.conformation.Residue method) type_set_mode_from_string() (in module pyrosetta.rosetta.core.chemical) type_set_tag() (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) type_string() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) types() (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.Patch method) types_to_avoid() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) TypeSetMode (class in pyrosetta.rosetta.core.chemical)

U

u() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) u_initialized() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) u_no_notify() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) ub() (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) ubyte (class in pyrosetta.rosetta.ObjexxFCL) UDPSocketClient (class in pyrosetta.rosetta.protocols.moves) uint_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) ulong_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) unassigned() (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) unbind() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) unblock() (pyrosetta.rosetta.utility.signals.Link method) unblock_signals() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) unbound_struct() (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) unbounded() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) unbounded_value() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) UnboundRotamersOperation (class in pyrosetta.rosetta.core.pack.rotamer_set) uncompressed() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) UnconstrainedTorsionsMover (class in pyrosetta.rosetta.protocols.ligand_docking) undefined_positions() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) unfinished_batches() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) unfolded_energies_type() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) UnfoldedStatePotential (class in pyrosetta.rosetta.core.scoring) unfreeze() (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) unget() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) uniform() (in module pyrosetta.rosetta.numeric.random) (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) uniform_dof_distribution() (in module pyrosetta.rosetta.protocols.simple_moves) uniform_RG (class in pyrosetta.rosetta.numeric.random) uniform_vector_sphere() (in module pyrosetta.rosetta.numeric.random) UniformPerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) UniformPolicy (class in pyrosetta.rosetta.protocols.nonlocal) UniformRotationMover (class in pyrosetta.rosetta.protocols.simple_moves) UniformSphereTransMover (class in pyrosetta.rosetta.protocols.rigid) UniformTranslationMover (class in pyrosetta.rosetta.protocols.simple_moves) union_interval() (in module pyrosetta.rosetta.protocols.forge.methods) union_of_intervals_containing_undefined_positions() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) unique() (in module pyrosetta.rosetta.ObjexxFCL) uniqued() (in module pyrosetta.rosetta.ObjexxFCL) universal_main() (in module pyrosetta.rosetta.protocols.jobdist) unlabel() (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) unpaired_valence_electrons_sp() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) unpatchable_residue_types() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) unperturbed_sequence() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) UnrecognizedAtomFeaturesCreator (class in pyrosetta.rosetta.protocols.features) UnrecognizedAtomRecord (class in pyrosetta.rosetta.core.pose) UnsatSelector (class in pyrosetta.rosetta.protocols.residue_selectors) unset_acceptor_ether_oxygens() (in module pyrosetta.rosetta.core.chemical) unset_native_pose() (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) unset_parent() (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap method) unsigned_periodic_range() (in module pyrosetta.rosetta.basic) unused_hbond() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) upcase() (in module pyrosetta.rosetta.ObjexxFCL) update() (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) (pyrosetta.rosetta.core.scoring.TMscoreStore method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) update_actcoord() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) update_actcoords() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) update_active_enmeths_for_residue() (pyrosetta.rosetta.core.scoring.MinimizationNode method) update_after_boltzmann() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) update_atom_information_based_on_occupancy() (in module pyrosetta.rosetta.core.io.pose_from_sfr) update_atom_map() (in module pyrosetta.rosetta.protocols.hybridization) update_atom_tree() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) update_chemshiftscore_from_peak() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) update_commutative() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) update_connections_to_other_residue() (pyrosetta.rosetta.core.conformation.Residue method) update_connectivity_data() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) update_constraint_set_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) update_coords_from_pose() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) update_counting_last_PDR() (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) update_cutpoint_virtual_atoms_if_connected() (in module pyrosetta.rosetta.core.conformation) (in module pyrosetta.rosetta.core.pose) update_derived_rna_data() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) update_disulfides_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) update_domain_map() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) update_edge_label() (pyrosetta.rosetta.core.kinematics.FoldTree method) update_enumeration_shell() (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) update_fixed_domain_from_extra_minimize_jump_res() (in module pyrosetta.rosetta.core.import_pose) update_fold_tree_at_virtual_sugars() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) update_from_momento() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) update_full_model_info_from_pose() (in module pyrosetta.rosetta.core.pose.full_model_info) update_internal_coords() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) update_intersection() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) update_jobs_list() (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) update_jump_atoms_for_mg_bound_water() (in module pyrosetta.rosetta.protocols.magnesium) update_jump_res() (in module pyrosetta.rosetta.core.import_pose) update_membrane_position() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) update_mg_hoh_fold_tree() (in module pyrosetta.rosetta.protocols.magnesium) update_noncanonical_connection() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) update_numbers_in_pdb_info() (in module pyrosetta.rosetta.protocols.magnesium) update_nus() (pyrosetta.rosetta.core.conformation.Residue method) update_on_length_change() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) update_one_body_energies() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) update_orbital_coords() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) update_partner_embeddings() (in module pyrosetta.rosetta.protocols.membrane) update_pdb_info_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) update_pdb_remarks() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) update_pdblist_file() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) update_polymer_bond_dependent_atoms() (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) update_polymer_dependent() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) update_polymeric_connection() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) update_pose_chains_from_pdb_chains() (pyrosetta.rosetta.core.pose.Pose method) update_pose_fold_tree() (in module pyrosetta.rosetta.core.import_pose) update_pose_objects_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) update_res_list_in_full_model_info_and_pdb_info() (in module pyrosetta.rosetta.core.pose.full_model_info) update_residue() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) update_residue_commutative() (pyrosetta.rosetta.core.pack.task.PackerTask_ method) update_residue_for_packing() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.FACTSPotential method) (pyrosetta.rosetta.core.scoring.GenBornPotential method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method)

update_residue_identities() (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) update_residue_intersection() (pyrosetta.rosetta.core.pack.task.PackerTask_ method) update_residue_links() (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) update_residue_neighbors() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) update_residue_union() (pyrosetta.rosetta.core.pack.task.PackerTask_ method) update_residue_variants() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) update_rna_base_base_interactions() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) update_rna_base_pair_list() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) update_rna_centroid_info() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) update_rot_trans_mag() (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) update_scores() (in module pyrosetta.rosetta.protocols.recces) update_sequence() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) update_sequence_numbering() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.kinematics.AtomTree method) update_start_position() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) update_stub() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) update_submotif_info_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) update_task_and_neighbors() (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) update_to_move_chunks_with_domain() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) update_to_move_rosetta_library_chunks() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) update_type() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) update_union() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) update_upperdistance_score() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) update_xyz_coords() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) UpdateEnzdesHeaderMover (class in pyrosetta.rosetta.protocols.enzdes) updates_jobs_list() (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) upper() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) upper_atom_neighbors() (pyrosetta.rosetta.core.scoring.NeighborList method) upper_bound() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) upper_bound_score() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) upper_chain() (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) upper_connect() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) upper_connect_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) upper_connect_id() (pyrosetta.rosetta.core.chemical.ResidueType method) upper_dihedrals() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) upper_edge_list_begin() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) upper_edge_list_end() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) upper_is_symm_equivalent_of_lower() (in module pyrosetta.rosetta.core.conformation) upper_local() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) upper_neighbor_id() (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) upper_neighbor_iterator_begin() (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) upper_neighbor_iterator_end() (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) upper_padding() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) upper_residue() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) upper_segment() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) upper_threshold() (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) upper_value() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) uppercase() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) uppercased() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) upstream_atom() (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.kinematics.FoldTree method) upstream_builder() (pyrosetta.rosetta.protocols.match.Matcher method) upstream_centroid_by_jump() (in module pyrosetta.rosetta.protocols.geometry) upstream_combine() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) upstream_jump_residue() (pyrosetta.rosetta.core.kinematics.FoldTree method) upstream_jump_stub() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) upstream_only() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) upstream_pose() (pyrosetta.rosetta.protocols.match.Matcher method) upstream_restypes() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) UpstreamCollisionFilter (class in pyrosetta.rosetta.protocols.match.output) UpstreamDownstreamCollisionFilter (class in pyrosetta.rosetta.protocols.match.output) UpstreamResTypeGeometry (class in pyrosetta.rosetta.protocols.match.upstream) urs_norm4() (in module pyrosetta.rosetta.numeric) urs_R2ang() (in module pyrosetta.rosetta.numeric) us_secmatch_hit_compare (class in pyrosetta.rosetta.protocols.match.downstream) use_average() (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) use_cartesian() (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) use_cartmin() (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) use_coarse_vdw() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) use_coordinate_constraints() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) use_default_membrane() (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) use_defaults() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) use_dssp() (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) use_extended_intrares_energy_interface() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) use_extended_residue_energy_interface() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) use_extended_residue_pair_energy_interface() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) use_fract_expected_values_any() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) use_fract_ranges() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) use_fract_ranges_any() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) use_fragments() (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) use_fullmer() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) use_gen_kirkwood() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) use_green_packer() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) use_input_for_ref() (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) USE_INPUT_SC (class in pyrosetta.rosetta.core.pack.task) use_late_scoring_for_zeros() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) use_loops_from_threading_job() (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) use_mover_status() (pyrosetta.rosetta.protocols.moves.SequenceMover method) use_multicool_annealer() (pyrosetta.rosetta.core.pack.task.operation.OptH method) use_nblist() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) use_nblist_auto_update() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) use_nblist_of_type() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) use_nobias() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) use_origseq_for_not_dsgned_layer() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) use_packer_instead_of_rotamer_trials() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) use_pdb_format_HETNAM_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) use_phenix_geo() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) use_polarization() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) use_pose_sequence_as_native() (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) use_prefiltering() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) use_preset_task() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) use_radial_lookup() (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) use_rama_2B() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) use_random_conformer() (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) use_rt() (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) use_sc_neighbors() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) user() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) user_chain1() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) user_chain2() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) user_options() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) user_or() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) user_provided_movers_apply_cycle() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) ushort_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) USOGFunc (class in pyrosetta.rosetta.core.scoring.func) uz() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method)

V

v_begin() (pyrosetta.rosetta.protocols.loops.Loops method) v_end() (pyrosetta.rosetta.protocols.loops.Loops method) valence_electrons_p() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) valence_electrons_s() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) valence_electrons_sp() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) valence_electrons_spd() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) valid() (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.JumpID method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.id.NamedStubID method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.nonlocal.Chunk method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator method) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.EdgeListIterator method) (pyrosetta.rosetta.utility.signals.Link method) valid_ends() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) valid_names_string() (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) valid_ss() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) validate() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) validate_beta() (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory method) validate_dunbrack_binary() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) validate_input_script_against_xsd() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) validate_loop_start_stop() (in module pyrosetta.rosetta.protocols.loops) validate_talaris() (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory method) validate_xml_against_xsd() (in module pyrosetta.rosetta.utility.tag) vall_key() (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) vall_library_from_file() (in module pyrosetta.rosetta.core.fragment.picking_old.vall) vall_memory_usage() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) VallChunk (class in pyrosetta.rosetta.protocols.frag_picker) VallChunkFilter (class in pyrosetta.rosetta.protocols.frag_picker) vallChunksFromLibraries() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) vallChunksFromLibrary() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) VallData (class in pyrosetta.rosetta.protocols.frags) VallFragmentEval (class in pyrosetta.rosetta.core.fragment.picking_old.vall.eval) VallFragmentGen (class in pyrosetta.rosetta.core.fragment.picking_old.vall.gen) VallFragmentScore (class in pyrosetta.rosetta.core.fragment.picking_old.vall.scores) VallLibrarian (class in pyrosetta.rosetta.core.fragment.picking_old.vall) VallLibrary (class in pyrosetta.rosetta.core.fragment.picking_old.vall) vallNumLines() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) VallProvider (class in pyrosetta.rosetta.protocols.frag_picker) VallResidue (class in pyrosetta.rosetta.core.fragment.picking_old.vall) (class in pyrosetta.rosetta.protocols.frag_picker) VallResidues (class in pyrosetta.rosetta.core.fragment.picking_old.vall) VallSection (class in pyrosetta.rosetta.core.fragment.picking_old.vall) VallSections (class in pyrosetta.rosetta.core.fragment.picking_old.vall) Value (class in pyrosetta.rosetta.utility.py) value() (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) value_deriv() (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) value_or() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) value_passes() (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator method) value_set() (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) value_string() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) Value_type (class in pyrosetta.rosetta.utility.json_spirit) ValueEvaluator (class in pyrosetta.rosetta.protocols.enzdes) ValueEvaluator.CompareMode (class in pyrosetta.rosetta.protocols.enzdes) variable_name() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) variant_type_enums() (pyrosetta.rosetta.core.chemical.ResidueType method) variant_types() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.pose.MiniPose method) variant_types_list() (pyrosetta.rosetta.core.pose.MiniPose method) variants_match() (in module pyrosetta.rosetta.core.chemical) variants_match_with_exceptions() (in module pyrosetta.rosetta.core.chemical) VariantType (class in pyrosetta.rosetta.core.chemical) VarLengthBuild (class in pyrosetta.rosetta.protocols.forge.components) vars_to_dofs() (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) VarSolDRotamerDots (class in pyrosetta.rosetta.protocols.vardist_solaccess) vary_polar_hydrogen_geometry() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) vary_rna_bond_geometry() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) vary_stepsize() (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) VaryLoopLengthMover (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) vdw_cached_rep_screen_info_is_setup() (in module pyrosetta.rosetta.protocols.scoring) vdw_calculation_annotated_sequence() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) VDW_rep_alignment_RMSD_CUTOFF() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) VDW_rep_delete_matching_res() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) VDW_rep_screen_info() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) VDW_rep_screen_physical_pose_clash_dist_cutoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) vdw_type() (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) VdWTinkerPoseInfo (class in pyrosetta.rosetta.core.scoring) VdWTinkerPotential (class in pyrosetta.rosetta.core.scoring) VdWTinkerResidueInfo (class in pyrosetta.rosetta.core.scoring) VdWTinkerRotamerSetInfo (class in pyrosetta.rosetta.core.scoring) vec3_to_stub() (in module pyrosetta.rosetta.protocols.sic_dock) vec_distance() (in module pyrosetta.rosetta.numeric.kdtree)

vector() (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) Vector1() (in module pyrosetta) vector1_indices() (in module pyrosetta.util) vector_angle_cut() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) vector_angle_cutoff() (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) vector_dist_cut() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) vector_dist_cutoff() (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) vector_has_n_trues() (in module pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster) vector_normal_to_ring_plane_of_best_fit() (in module pyrosetta.rosetta.numeric.geometry) vector_to_rank() (in module pyrosetta.rosetta.protocols.ligand_docking) VectorOption (class in pyrosetta.rosetta.utility.options) VectorOptionKey (class in pyrosetta.rosetta.utility.options) VectorPoseMover (class in pyrosetta.rosetta.protocols.moves) vectorsEqual() (in module pyrosetta.rosetta.numeric.kinematic_closure) ver() (pyrosetta.rosetta.utility.file.FileName method) verbose() (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) verbose_sampler() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) verify_against() (pyrosetta.rosetta.protocols.loops.Loops method) version() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.utility.file.FileName method) vertex() (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) vertex_already_reached() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) vertex_count() (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) vertex_exists() (in module pyrosetta.rosetta.protocols.forge.methods) vertex_xyz_from_generators() (in module pyrosetta.rosetta.core.scoring.power_diagram) vertices() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) VicinityPerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) VicinitySamplingKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) view_constraints_in_pymol() (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) virtual_sidechain() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) virtual_sugar_do_minimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) virtual_sugar_do_screens() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) virtual_sugar_keep_base_fixed() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) virtual_sugar_legacy_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) virtual_to_real() (pyrosetta.rosetta.core.pose.Pose method) virtual_type_for_conf() (in module pyrosetta.rosetta.core.conformation) virtual_type_for_pose() (in module pyrosetta.rosetta.core.pose) virtualize_5prime_phosphates() (in module pyrosetta.rosetta.core.pose.rna) virtualize_bulges() (in module pyrosetta.rosetta.protocols.rna.denovo) virtualize_free_rna_moieties() (in module pyrosetta.rosetta.core.pose.rna) virtualize_packable_moieties_in_screening_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) virtualize_side_chains() (in module pyrosetta.rosetta.protocols.stepwise.modeler) VirtualizeAll (class in pyrosetta.rosetta.core.chemical) VirtualizeSidechain (class in pyrosetta.rosetta.core.chemical) visible() (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerImpl method) visit() (pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser method) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter method) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) visualize_fold_tree() (in module pyrosetta.rosetta.core.kinematics) visualize_voxel_grid() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) VisualizeEmbeddingMover (class in pyrosetta.rosetta.protocols.membrane.visualize) VisualizeEmbeddingMoverCreator (class in pyrosetta.rosetta.protocols.membrane.visualize) VisualizeMembraneMover (class in pyrosetta.rosetta.protocols.membrane.visualize) VisualizeMembraneMoverCreator (class in pyrosetta.rosetta.protocols.membrane.visualize) vl_vh_orientation_coords() (in module pyrosetta.rosetta.protocols.antibody) VLB (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) vlb() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) VMaxBy (class in pyrosetta.rosetta.protocols.pack_daemon) VMinBy (class in pyrosetta.rosetta.protocols.pack_daemon) voids_penalty_energy_cone_distance_cutoff() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) voids_penalty_energy_cone_dotproduct_cutoff() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) voids_penalty_energy_containing_cones_cutoff() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) voids_penalty_energy_disabled_except_during_packing() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) voids_penalty_energy_voxel_grid_padding() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) voids_penalty_energy_voxel_size() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) VoidsPenaltyEnergy (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy) VoidsPenaltyVoxelGrid (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy) vol() (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) volume() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) VoxelSetIterator (class in pyrosetta.rosetta.protocols.match) VoxelSpacingMultifunc (class in pyrosetta.rosetta.protocols.electron_density) VoxelSpacingRefinementMover (class in pyrosetta.rosetta.protocols.electron_density) vrt1() (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) vrt2() (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method)

W

w() (in module pyrosetta.rosetta.numeric.statistics) w_im() (in module pyrosetta.rosetta.numeric.statistics) wait_for_remote_vars() (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) waiting_on_dependencies() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) WalkingBondAnglePerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) WalkingPerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) WallpaperGroupSetting (class in pyrosetta.rosetta.protocols.cryst) Warning() (in module pyrosetta.rosetta.basic) was_init_called() (in module pyrosetta.rosetta.basic) was_modified() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) was_successful() (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) water_adduct_hbond_score() (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) water_dielectric() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) water_specific_hbond_energy() (in module pyrosetta.rosetta.protocols.hydrate) WaterAdductHBondPotential (class in pyrosetta.rosetta.core.scoring) WaterBuilder (class in pyrosetta.rosetta.core.scoring.lkball) WaterFeaturesCreator (class in pyrosetta.rosetta.protocols.features) weight() (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.core.scoring.AtomNeighbor method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) weight_func() (pyrosetta.rosetta.core.scoring.AtomNeighbor method) weighted_string_of() (pyrosetta.rosetta.core.scoring.EMapVector method) weights() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) weights_for_hbonds() (in module pyrosetta.rosetta.core.scoring.hbonds) wfa_atr() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) wfa_rep() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) wfa_sol() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) what() (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.utility.excn.BadInput method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) whatIsTooSmall() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) which_atom_in_hbond (class in pyrosetta.rosetta.core.scoring.hbonds) which_glycosidic_torsion() (in module pyrosetta.rosetta.core.pose.carbohydrates) which_point_for_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) which_torsions() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) whoami() (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) whole_pose_context_enmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationGraph method) whole_pose_context_enmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationGraph method) whole_structure_types() (pyrosetta.rosetta.core.scoring.ScoreFunction method) WholeBodyRotationMover (class in pyrosetta.rosetta.protocols.rigid) WholeBodyTranslationMover (class in pyrosetta.rosetta.protocols.rigid) WholeStructureEnergy (class in pyrosetta.rosetta.core.scoring.methods) widget_name() (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator method) width() (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) WidthFirstSlidingWindowLoopClosure (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) wipe_out_moving_residues() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) within1bonds_sets_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) within2bonds_sets_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) WobbleMover (class in pyrosetta.rosetta.protocols.simple_moves) working_pack_res() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) working_pack_res_was_inputted() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) working_parameters() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) working_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) WorkUnit_bbGauss (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_CombinePose (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_FragInsert (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_KicCloser (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_LoopHash (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_MD (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_MoverWrapper (class in pyrosetta.rosetta.protocols.wum) WorkUnit_NormalMode (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_PartialAbinitio (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_RamaPerturber (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_Relax (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_SilentStructStore (class in pyrosetta.rosetta.protocols.wum) WorkUnitBase (class in pyrosetta.rosetta.protocols.wum) WorkUnitList (class in pyrosetta.rosetta.protocols.wum) worst_distance() (pyrosetta.rosetta.numeric.kdtree.KDPointList method) Wradius() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) wrapped() (pyrosetta.rosetta.utility.options.OptionCollection method) WrapperOptEMultifunc (class in pyrosetta.rosetta.protocols.optimize_weights) write() (in module pyrosetta.rosetta.utility.json_spirit) (pyrosetta.logging_support.PythonLoggingSink method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.Report method) (pyrosetta.rosetta.basic.TracerImpl method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) write2pdb() (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) write_3Dprojection_kinemage() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) write_AA_distribution_with_direction_to_a_file() (in module pyrosetta.rosetta.protocols.features.strand_assembly) write_AA_distribution_without_direction_to_a_file() (in module pyrosetta.rosetta.protocols.features.strand_assembly) write_AA_kind_to_a_file() (in module pyrosetta.rosetta.protocols.features.strand_assembly) write_ab_H3_kink_metrics_schema_to_db() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method)

write_ab_metrics_schema_to_db() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) write_all() (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) write_all_connect_info() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) write_assignments() (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) write_batch_reports_table() (in module pyrosetta.rosetta.protocols.features) write_binary() (in module pyrosetta.rosetta.core.io.serialization) write_binary_chars() (in module pyrosetta.rosetta.core.io.serialization) write_cdr_metrics_schema_to_db() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) write_cdr_residue_schema_to_db() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) write_chain_B_resNum_to_a_file() (in module pyrosetta.rosetta.protocols.features.strand_assembly) write_checkpoint() (in module pyrosetta.rosetta.protocols.dna) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) write_circle_intersection_mask_to_kinemage() (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) write_comment() (pyrosetta.rosetta.core.io.silent.SilentFileData method) write_complex_type_to_schema() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) write_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) write_crick_params_file_data() (in module pyrosetta.rosetta.protocols.helical_bundle) write_db() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) write_definition() (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement method) write_dot_kinemage() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) write_downstream_coordinates() (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) write_eggshell_to_pdb() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) write_exposed_dots_to_kinemage() (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) write_features_reporters_table() (in module pyrosetta.rosetta.protocols.features) write_formatted() (in module pyrosetta.rosetta.utility.json_spirit) write_glycan_pdb_codes() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) write_graphviz() (in module pyrosetta.rosetta.core.chemical) write_Grid_to_pdb() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) write_grids() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) write_hashing_scores_to_file() (in module pyrosetta.rosetta.protocols.legacy_sewing) write_info_file() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) write_interface_residues_schema_to_db() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) write_interface_schema_to_db() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) write_interface_side_schema_to_db() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) write_kinemage_header() (in module pyrosetta.rosetta.core.conformation) write_lines() (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) write_loops_to_file() (pyrosetta.rosetta.protocols.loops.Loops method) write_loops_to_stream() (pyrosetta.rosetta.protocols.loops.Loops method) write_match_groups() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) write_match_scores() (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) write_metric_value() (in module pyrosetta.rosetta.basic) write_minor_helix_params() (in module pyrosetta.rosetta.protocols.helical_bundle) write_model_file() (in module pyrosetta.rosetta.protocols.legacy_sewing) write_motifs_binary() (in module pyrosetta.rosetta.core.scoring.motif) write_number_of_electrostatic_interactions_of_residues_to_files() (in module pyrosetta.rosetta.protocols.features.strand_assembly) write_output() (pyrosetta.rosetta.protocols.jd3.output.ResultOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter method) write_p_aa_pp_of_AAs_to_a_file() (in module pyrosetta.rosetta.protocols.features.strand_assembly) write_pdb_link_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) write_pdb_parametric_info() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) write_phipsi() (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) write_pocketGrid_to_pdb() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) write_psipred_ss2() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) write_pymol_string_to_pdb() (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) write_rama_of_AAs_to_a_file() (in module pyrosetta.rosetta.protocols.features.strand_assembly) write_ROSETTASCRIPTS_complex_type() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) write_schema_to_database() (in module pyrosetta.rosetta.basic.database) write_schema_to_db() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) write_score_function_method_options_table_schema() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) write_score_tracer() (in module pyrosetta.rosetta.protocols.jd2) write_scorefile() (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) write_silent_struct() (pyrosetta.rosetta.core.io.silent.SilentFileData method) write_talos_format() (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) write_to_binary_file() (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) write_to_disk() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) write_to_file() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) write_to_pdb() (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) write_to_stream() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) write_topology_file() (in module pyrosetta.rosetta.core.chemical) write_xfres_binary() (in module pyrosetta.rosetta.core.scoring.motif) WriteableCacheableData (class in pyrosetta.rosetta.basic.datacache) WriteableCacheableDataCreator (class in pyrosetta.rosetta.basic.datacache) WriteableCacheableMap (class in pyrosetta.rosetta.basic.datacache) WriteFiltersToPose (class in pyrosetta.rosetta.protocols.simple_moves) WriteSSEMover (class in pyrosetta.rosetta.protocols.simple_moves) WriteToDB_AA_to_terminal_loops() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_avg_b_factor_CB_at_each_component() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_dihedral_angle_between_core_strands_across_facing_sheets() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_dssp_ratio_in_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_ending_loop() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_hydrophobic_ratio_net_charge() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_long_strand_id_in_each_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_min_avg_dis_between_sheets_by_cen_res() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_min_dis_between_sheets_by_all_res() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_number_of_core_heading_aro_AAs_in_a_pair_of_edge_strands() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_number_of_core_heading_charged_AAs_in_a_pair_of_edge_strands() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_number_of_core_heading_FWY_in_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_number_of_core_heading_LWY_in_core_strands_in_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_number_of_core_heading_W_in_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_number_of_edge_strands_in_each_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_number_of_sheets_that_surround_this_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_number_strands_in_each_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_prolines_that_seem_to_prevent_aggregation() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_ratio_of_core_heading_FWY_in_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_rkde() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_rkde_in_strands() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_sandwich() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_sandwich_by_AA_w_direction() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_sheet_antiparallel() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_sheet_connectivity() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_sheet_id() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_shortest_dis_between_facing_aro_in_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_starting_loop() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_sw_can_by_sh() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_sw_res_size() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_topology_candidate() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_turn_AA() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_turn_type() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_whether_sw_is_not_connected_with_continuous_atoms() (in module pyrosetta.rosetta.protocols.features.strand_assembly) ws_methods_begin() (pyrosetta.rosetta.core.scoring.ScoreFunction method) ws_methods_end() (pyrosetta.rosetta.core.scoring.ScoreFunction method) wt_aa() (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) WUM_MPI_TAGS (class in pyrosetta.rosetta.protocols.wum) wwPDBJobOutputter (class in pyrosetta.rosetta.protocols.jd2)

X

x() (in module pyrosetta.rosetta.numeric.crick_equations) X() (in module pyrosetta.rosetta.ObjexxFCL.format) x() (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) x0() (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) X11Colors (class in pyrosetta.rosetta.protocols.moves) X_BUNDLE() (in module pyrosetta.rosetta.numeric.crick_equations) xd() (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) xform_pose() (in module pyrosetta.rosetta.core.fragment) (in module pyrosetta.rosetta.core.scoring.motif) (in module pyrosetta.rosetta.protocols.sic_dock) xform_pose_rev() (in module pyrosetta.rosetta.protocols.sic_dock) xm() (pyrosetta.rosetta.numeric.model_quality.RmsData method) xml_schema_attributes() (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) XMLSchemaAttribute (class in pyrosetta.rosetta.utility.tag) XMLSchemaCommonType (class in pyrosetta.rosetta.utility.tag) XMLSchemaComplexType (class in pyrosetta.rosetta.utility.tag) XMLSchemaComplexTypeGenerator (class in pyrosetta.rosetta.utility.tag) XMLSchemaDataType (class in pyrosetta.rosetta.utility.tag) XMLSchemaDefinition (class in pyrosetta.rosetta.utility.tag) XMLSchemaElement (class in pyrosetta.rosetta.utility.tag) XMLSchemaElementCategory (class in pyrosetta.rosetta.utility.tag) XMLSchemaMinOccursMaxOccurs (class in pyrosetta.rosetta.utility.tag) XMLSchemaModelGroup (class in pyrosetta.rosetta.utility.tag) XMLSchemaModelGroupType (class in pyrosetta.rosetta.utility.tag) XMLSchemaParticle (class in pyrosetta.rosetta.utility.tag) XMLSchemaRestriction (class in pyrosetta.rosetta.utility.tag) XMLSchemaRestrictionType (class in pyrosetta.rosetta.utility.tag) XMLSchemaSimpleSubelementList (class in pyrosetta.rosetta.utility.tag) XMLSchemaTopLevelElement (class in pyrosetta.rosetta.utility.tag) XMLSchemaType (class in pyrosetta.rosetta.utility.tag) xn() (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) xre() (pyrosetta.rosetta.numeric.model_quality.RmsData method) xrp() (pyrosetta.rosetta.numeric.model_quality.RmsData method) xs_model_group_name() (in module pyrosetta.rosetta.utility.tag) xsd_architect_type_definition_w_attributes() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) xsd_for_rosetta_scripts() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) xsd_simple_metric_type_definition_w_attributes() (in module pyrosetta.rosetta.core.simple_metrics) xsd_type_definition_w_attributes() (in module pyrosetta.rosetta.basic.resource_manager.locator) (in module pyrosetta.rosetta.core.select.jump_selector) (in module pyrosetta.rosetta.core.select.residue_selector) (in module pyrosetta.rosetta.protocols.features) (in module pyrosetta.rosetta.protocols.filters) (in module pyrosetta.rosetta.protocols.loops.loops_definers) (in module pyrosetta.rosetta.protocols.moves) (in module pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster) (in module pyrosetta.rosetta.protocols.qsar.scoring_grid) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method)

xsd_type_definition_w_attributes_and_optional_subselector() (in module pyrosetta.rosetta.core.select.jump_selector) (in module pyrosetta.rosetta.core.select.residue_selector) xsd_type_definition_w_attributes_and_optional_subselectors() (in module pyrosetta.rosetta.core.select.jump_selector) (in module pyrosetta.rosetta.core.select.residue_selector) xsd_type_definition_w_attributes_and_repeatable_subelements() (in module pyrosetta.rosetta.basic.resource_manager.locator) (in module pyrosetta.rosetta.protocols.features) (in module pyrosetta.rosetta.protocols.filters) (in module pyrosetta.rosetta.protocols.moves) xse() (pyrosetta.rosetta.numeric.model_quality.RmsData method) xsp() (pyrosetta.rosetta.numeric.model_quality.RmsData method) xyz() (in module pyrosetta.rosetta.numeric.crick_equations) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.conformation.Atom method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc method) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) XYZ_BUNDLE() (in module pyrosetta.rosetta.numeric.crick_equations) xyz_from_internal_coords() (in module pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover) XYZ_Func (class in pyrosetta.rosetta.core.scoring.func) xyz_gdtmm() (in module pyrosetta.rosetta.core.scoring) xyz_gdttm() (in module pyrosetta.rosetta.core.scoring) xyz_maxsub() (in module pyrosetta.rosetta.core.scoring) xyz_to_vec1() (in module pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover) XYZEvent (class in pyrosetta.rosetta.core.conformation.signals)

Y

y() (in module pyrosetta.rosetta.numeric.crick_equations) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method)

Y_BUNDLE() (in module pyrosetta.rosetta.numeric.crick_equations) YamlEmitter (class in pyrosetta.rosetta.basic)

Z

z() (in module pyrosetta.rosetta.numeric.crick_equations) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) z0_offset() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) z1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) z1_offset() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) z_axis_dist() (in module pyrosetta.rosetta.protocols.dna) Z_BUNDLE() (in module pyrosetta.rosetta.numeric.crick_equations) z_rotation_matrix() (in module pyrosetta.rosetta.numeric) z_rotation_matrix_degrees() (in module pyrosetta.rosetta.numeric) ZERO() (in module pyrosetta.rosetta.core.kinematics) zero() (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.scoring.EMapVector method) zero_one_body_energies_for_node() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) zero_one_body_energy_for_node_state() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) zero_reference_pose_mapping_at_seqpos() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method)

zero_torsion_vectors() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) zeroAngle() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) zeta() (pyrosetta.rosetta.core.pose.Pose method) zeta_aform() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) zflush() (pyrosetta.rosetta.utility.io.ozstream method) zflush_finalize() (pyrosetta.rosetta.utility.io.ozstream method) ZincHeterodimerMover (class in pyrosetta.rosetta.protocols.metal_interface) zoom() (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) Zscore_to_library() (in module pyrosetta.rosetta.protocols.mpi_refinement) zvalue() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method)