Index – 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.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_score_convergence_threshold() (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) abs_score_diff_after_minimization() (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.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.simple_moves.GenericSimulatedAnnealer method) accept_counter() (pyrosetta.rosetta.protocols.simple_moves.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.simple_moves.GenericSimulatedAnnealer method) AcceptedScores (class in pyrosetta.rosetta.protocols.simple_moves) acceptor_selector() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter 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.simple_moves.GenericSimulatedAnnealer method) adaptive() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) adaptive_movers() (pyrosetta.rosetta.protocols.simple_moves.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.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_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.protocols.rna.denovo.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.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) 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.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.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) add_edges_from_binary() (pyrosetta.rosetta.protocols.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.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.simple_filters.Operator method) (pyrosetta.rosetta.protocols.simple_moves.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.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues method) add_groupD() (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) add_groupE() (pyrosetta.rosetta.protocols.simple_moves.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.simple_moves.CstInfoMover method) add_init_dev_penalty() (in module pyrosetta.rosetta.protocols.mpi_refinement) add_inputvalue() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) add_job_data_to_ss() (in module pyrosetta.rosetta.protocols.jd2) add_job_options() (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) 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_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.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.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly 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.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.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.toolbox.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.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_Illegal_Arguments 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.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.utility.excn.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_new_cluster() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) add_new_data() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) 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.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_option() (pyrosetta.rosetta.basic.resource_manager.JobOptions 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_atoms_to_network_state() (in module pyrosetta.rosetta.protocols.hbnet) 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_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.toolbox.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_resource_configuration() (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) add_resource_locator() (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) add_resource_options() (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) add_resource_tag_by_job_tag() (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) 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_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_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_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_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.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.toolbox.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation method) add_to_energy_map() (pyrosetta.rosetta.core.scoring.EnergyEdge method) 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) 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.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.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.VirtualizeAll 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.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.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) addScoresForLoopParts() (in module pyrosetta.rosetta.protocols.loops) AddSegmentDataMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) 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) 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.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.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) AlignChainMover (class in pyrosetta.rosetta.protocols.simple_moves)

AlignedThreadOperation (class in pyrosetta.rosetta.protocols.toolbox.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.toolbox.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) 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.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.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.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) all_target_res() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) all_tracers() (pyrosetta.rosetta.basic.TracerManager 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.toolbox.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.toolbox.task_operations.SelectResiduesWithinChainOperation method) allow_design_around() (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.toolbox.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.toolbox.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) analyze_base_bin_map() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body) 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_extrachi_cutoff() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ 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_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_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) 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) 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) 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_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.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.simple_moves.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.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) append_name_and_attributes_to_complex_type() (in module pyrosetta.rosetta.utility.tag) 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_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_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_segments() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.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.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.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.VirtualizeAll 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.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.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.VirtualizeAll 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.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.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.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.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.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.InterfaceAnalyzerMover 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.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.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax 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.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator 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.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.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.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator 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.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.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.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.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.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_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile 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.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.simple_filters.Operator 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.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter 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.ConsensusDesignMover 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.CstInfoMover 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.DesignRepackMover 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.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover 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.RotamerizeMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover 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.TaskAwareMinMover 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.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_moves.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover 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.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation 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.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_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.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_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.sewing.AssemblyConstraintsMover 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.simple_moves.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_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) 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.sewing) AssemblyConstraintsMover (class in pyrosetta.rosetta.protocols.sewing) AssemblyFactory (class in pyrosetta.rosetta.protocols.sewing) assert_phosphate_nomenclature_matches_mini() (in module pyrosetta.rosetta.protocols.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.W128_T 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.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.FallbackConfiguration method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator method) (pyrosetta.rosetta.basic.resource_manager.JobOptions method) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration 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.ResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator 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.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_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.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.VirtualizeAll 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_Illegal_Arguments 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.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.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.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.SilentFileLoaderCreator method) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator 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.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.AUTO 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.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.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.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.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.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.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.electron_density.ElectronDensityLoaderCreator method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator 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.fiber_diffraction.FiberDiffractionOptionsCreator 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.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.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.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.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.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.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.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.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.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.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceData method) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData 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.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.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax 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.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator 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.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.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.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.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.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.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.hbond_net_struct method) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct 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.JD2ResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator 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.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.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.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap 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.LoopsFileFallbackConfiguration method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileIO method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator 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.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.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.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.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.FragSetLoader method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader 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_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.base_pairs.BasePairStep 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.fragments.FullAtomRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler 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.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.sewing.Basis method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.sewing.Hasher method) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator 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.AcceptedScores 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.ConsensusDesignMover 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.CstInfoMover 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.DesignRepackMover 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.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover 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.RotamerizeMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover 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.TaskAwareMinMover 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.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_moves.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover 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.toolbox.AtomLevelDomainMap 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.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator 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.toolbox.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation 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.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.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.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_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_lower() (pyrosetta.rosetta.core.conformation.Residue method) atom_depends_on_upper() (pyrosetta.rosetta.core.conformation.Residue 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.protocols.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_virtual() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) atom_iterators() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_level_domain_map() (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) atom_map_from_score_result() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.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.protocols.rna.denovo.libraries.RNA_PairingTemplate method) atom_name2() (pyrosetta.rosetta.protocols.rna.denovo.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_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.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.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy 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.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy 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.protocols.toolbox) 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_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) 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) 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.simple_filters.Operator method) (pyrosetta.rosetta.protocols.simple_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() (in module pyrosetta.rosetta.core.pose) attributes_for_get_resnum_list() (in module pyrosetta.rosetta.core.pose) attributes_for_get_score_function_name() (in module pyrosetta.rosetta.protocols.rosetta_scripts) attributes_for_get_score_function_name_w_description() (in module pyrosetta.rosetta.protocols.rosetta_scripts) 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_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_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_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.protocols.rosetta_scripts) attributes_for_parse_score_function_w_description() (in module pyrosetta.rosetta.protocols.rosetta_scripts) attributes_for_parse_score_function_w_description_when_required() (in module pyrosetta.rosetta.protocols.rosetta_scripts) attributes_for_parse_task_operations() (in module pyrosetta.rosetta.protocols.rosetta_scripts) attributes_for_parse_task_operations_w_factory() (in module pyrosetta.rosetta.protocols.rosetta_scripts) 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) 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) AxEqDesignation (class in pyrosetta.rosetta.core.chemical.rings) axis() (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method)