Index – R

R() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) r0() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) r1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) r1_vect() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) R2quat() (in module pyrosetta.rosetta.protocols.simple_filters) rad() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) rad2() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) radial_bin_index() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) radial_count() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) radial_disp() (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) radial_lookup() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) radial_lookup_withkey() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) radians() (in module pyrosetta.rosetta.numeric.conversions) radius_for_attype() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) RadiusOfGyrationFeaturesCreator (class in pyrosetta.rosetta.protocols.features) rama() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) Rama2bPerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) rama_cutoff_energy() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) rama_delta() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) rama_prepro_multiplier() (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) RamaMutationSelector (class in pyrosetta.rosetta.protocols.cyclic_peptide) RamaPerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) RamaPreproFilename (class in pyrosetta.rosetta.core.chemical) RamaPreproResname (class in pyrosetta.rosetta.core.chemical) RamaScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) ramp_down_constraints() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) ramp_minpack_loop() (in module pyrosetta.rosetta.protocols.mpi_refinement) ramp_minpack_pose() (in module pyrosetta.rosetta.protocols.mpi_refinement) rand_sleep() (in module pyrosetta.rosetta.utility) random() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) random_angle() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) random_chunk_insertion() (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) random_connection() (in module pyrosetta.rosetta.protocols.ligand_docking) random_delay() (in module pyrosetta.rosetta.core.init) random_entity() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) random_fragment_insertion() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) random_mode() (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) random_mover() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) random_normal() (in module pyrosetta.rosetta.numeric.random) random_perturbation() (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) random_range() (in module pyrosetta.rosetta.numeric.random) (pyrosetta.rosetta.numeric.random.RandomGenerator method) random_range2() (pyrosetta.rosetta.numeric.random.RandomGenerator method) random_reorientation_matrix() (in module pyrosetta.rosetta.protocols.geometry) random_rotation() (in module pyrosetta.rosetta.core.scoring.motif) (in module pyrosetta.rosetta.numeric.random) random_torsion_move() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) random_trans() (pyrosetta.rosetta.core.kinematics.Jump method) random_tree_from_jump_points() (pyrosetta.rosetta.core.kinematics.FoldTree method) random_vector() (in module pyrosetta.rosetta.numeric.random) random_vector_spherical() (in module pyrosetta.rosetta.numeric.random) random_vector_unit_cube() (in module pyrosetta.rosetta.numeric.random) random_xform() (in module pyrosetta.rosetta.numeric.random) randomAngle() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) RandomConformerMover (class in pyrosetta.rosetta.protocols.ligand_docking) RandomGapSolutionPicker (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers) RandomGenerator (class in pyrosetta.rosetta.numeric.random) RandomGlycanFoliageSelector (class in pyrosetta.rosetta.core.select.residue_selector) randomize() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) randomize_glycan_torsions() (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) randomize_loop() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) randomize_loops() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) randomize_missing_coords() (in module pyrosetta.rosetta.core.io.pose_from_sfr) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) randomize_pose_rigid_bodies() (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) randomize_selected_atoms() (in module pyrosetta.rosetta.protocols.comparative_modeling) randomize_stage() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) RandomMover (class in pyrosetta.rosetta.protocols.moves) RandomMutation (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) RandomOmegaFlipMover (class in pyrosetta.rosetta.protocols.simple_moves) RandomPositionRotationMover (class in pyrosetta.rosetta.protocols.membrane) RandomPositionTranslationMover (class in pyrosetta.rosetta.protocols.membrane) RandomResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) RandomSheetBuilder (class in pyrosetta.rosetta.protocols.jumping) RandomSolutions (class in pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers) RandomTorsionMover (class in pyrosetta.rosetta.protocols.simple_moves) RandomTorsionPoseFolder (class in pyrosetta.rosetta.protocols.denovo_design.components) range() (in module pyrosetta.rosetta.protocols.sic_dock) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) range_check() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) rank_score() (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) RationalLoopComparator (class in pyrosetta.rosetta.protocols.loops) RationalMonteCarlo (class in pyrosetta.rosetta.protocols.simple_moves.rational_mc) raw_child_index() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_default_string() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) raw_get_nonjump_atom() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_input_stub_atom0() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_input_stub_atom1() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_input_stub_atom2() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_input_stub_atom3() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_parent() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_previous_child() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_previous_sibling() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_select() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) raw_stub_atom1() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_stub_atom2() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_stub_atom3() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_unfolded_state_energymap() (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential method) raw_value_string() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) RawFileData (class in pyrosetta.rosetta.core.io.raw_data) RawStruct (class in pyrosetta.rosetta.core.io.raw_data) rb_grid_rotamer_trials_atr_rep() (in module pyrosetta.rosetta.protocols.ligand_docking) rb_grid_score_atr_rep() (in module pyrosetta.rosetta.protocols.ligand_docking) rb_jump() (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) RB_lt (class in pyrosetta.rosetta.protocols.rbsegment_relax) rb_minimizable() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) rb_minimize_all_confs() (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) RBResidueRange (class in pyrosetta.rosetta.protocols.rbsegment_relax) RBSegment (class in pyrosetta.rosetta.protocols.rbsegment_relax) RBSegmentMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) RBSegmentRelax_main() (in module pyrosetta.rosetta.protocols) RBSegmentType (class in pyrosetta.rosetta.protocols.rbsegment_relax) rdbuf() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) RDC (class in pyrosetta.rosetta.core.scoring) RDC_Rohl (class in pyrosetta.rosetta.core.scoring) RdcEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) RDCScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) RdcSelectEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) RdcTargetEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) rdf_function_ct_namer() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) rdf_function_group_name() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) RDFBinaryHbondCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFBinaryHbondFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFBinaryHbondFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFBinaryOrbitalFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFBinaryOrbitalFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFBinaryOrbitalFunctionCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFChargeCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFChargeFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFChargeFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFElecCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFElecFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFElecFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFEtableCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFEtableFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFEtableFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFFunctionCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFFunctionFactory (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFHbondCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFHbondFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFHbondFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFOrbitalFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFOrbitalFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFOrbitalFunctionCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) read() (in module pyrosetta.rosetta.ObjexxFCL) (in module pyrosetta.rosetta.utility.json_spirit) (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) read_additional_pdb_data() (in module pyrosetta.rosetta.core.import_pose) read_alignment_file() (in module pyrosetta.rosetta.core.sequence) read_all_alignments() (in module pyrosetta.rosetta.core.sequence) read_all_poses() (in module pyrosetta.rosetta.core.import_pose) read_aln() (in module pyrosetta.rosetta.core.sequence) read_alternative_3_letter_codes_from_database_file() (in module pyrosetta.rosetta.core.io) read_anchorfile() (pyrosetta.rosetta.protocols.anchored_design.Anchor method) read_binary() (in module pyrosetta.rosetta.core.io.serialization) read_biounit() (in module pyrosetta.rosetta.protocols.sic_dock) read_bond_file() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) read_center_normal_from_cmd() (in module pyrosetta.rosetta.protocols.membrane) read_center_normal_from_tag() (in module pyrosetta.rosetta.protocols.membrane) read_checkpoint() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) read_codes_and_roots_from_database_file() (in module pyrosetta.rosetta.core.chemical.carbohydrates) read_comment_pdb() (in module pyrosetta.rosetta.core.pose) read_config_file() (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) read_conformers_from_database_file_for_ring_size() (in module pyrosetta.rosetta.core.chemical.rings) read_constraint() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) read_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) read_constraints_new() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) read_cp_tables_from_db() (in module pyrosetta.rosetta.core.scoring.elec) read_data() (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) read_db() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) read_ddg_predictions_file() (in module pyrosetta.rosetta.core.io.PositionDdGInfo) read_def() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) read_depth() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_disulf_pairing_list() (in module pyrosetta.rosetta.protocols.jumping) read_enzyme_data_from_file() (in module pyrosetta.rosetta.core.enzymes) read_fasta_file() (in module pyrosetta.rosetta.core.sequence) read_fasta_file_and_concatenate() (in module pyrosetta.rosetta.core.sequence) read_fasta_file_return_str() (in module pyrosetta.rosetta.core.sequence) read_fasta_file_section() (in module pyrosetta.rosetta.core.sequence) read_fasta_file_str() (in module pyrosetta.rosetta.core.sequence) read_file() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.ElementSet method) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) read_file_into_string() (in module pyrosetta.rosetta.protocols.cyclic_peptide_predict) read_files_for_base_residue_types() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) read_files_for_unpatchable_residue_types() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) read_fold_tree() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) read_fold_tree_from_file() (in module pyrosetta.rosetta.protocols.backrub) read_fragment_file() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) read_fragment_stream() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) read_from_binary_file() (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) read_from_disk() (pyrosetta.rosetta.protocols.sewing.Hasher method) read_from_file() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) read_from_file_no_filters() (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) read_from_stream() (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) read_Gaussian_parameters_from_database_file() (in module pyrosetta.rosetta.core.scoring.carbohydrates) read_general_aln() (in module pyrosetta.rosetta.core.sequence) read_general_aln_file() (in module pyrosetta.rosetta.core.sequence) read_glycan_sequence_file() (in module pyrosetta.rosetta.core.chemical.carbohydrates) read_grishin_aln_file() (in module pyrosetta.rosetta.core.sequence) read_H3_cter_fragment() (in module pyrosetta.rosetta.protocols.antibody_legacy) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) read_hyfile() (in module pyrosetta.rosetta.protocols.hydrate) read_in_amoeba_parameters() (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) read_in_and_recursively_replace_includes() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) read_in_and_set_disulfides() (pyrosetta.rosetta.core.io.raw_data.DisulfideFile method) read_in_structures() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) read_in_vdw_tinker_parameters() (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) read_individual_constraint_new() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) read_info_file() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) read_legacydb() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) read_loop_file() (pyrosetta.rosetta.protocols.loops.LoopsFileIO method) read_loop_file_stream() (pyrosetta.rosetta.protocols.loops.LoopsFileIO method) read_loop_fragments() (in module pyrosetta.rosetta.protocols.loops) read_loops_file() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) read_loops_options() (pyrosetta.rosetta.protocols.loops.Loops method) read_mArray() (in module pyrosetta.rosetta.utility.json_spirit) read_meta_file() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) read_metric_value() (in module pyrosetta.rosetta.basic) read_minor_helix_params() (in module pyrosetta.rosetta.protocols.helical_bundle) read_mObject() (in module pyrosetta.rosetta.utility.json_spirit) read_model_file() (in module pyrosetta.rosetta.protocols.sewing) read_motifs_binary() (in module pyrosetta.rosetta.core.scoring.motif) read_mover_weight() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) read_nomenclature_table_from_database_file() (in module pyrosetta.rosetta.core.chemical.carbohydrates) read_options() (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) read_or_throw() (in module pyrosetta.rosetta.utility.json_spirit) read_pairing_list() (in module pyrosetta.rosetta.core.scoring.dssp) read_params() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) read_pdb_header() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) read_peptide_design_file() (in module pyrosetta.rosetta.protocols.cyclic_peptide_predict) read_pose() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) read_pose_from_file() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) read_pose_numbered_loops_file() (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader method) read_probabilities_or_die() (in module pyrosetta.rosetta.numeric) read_psipred_ss2() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_psipred_ss2_file() (in module pyrosetta.rosetta.core.pose) read_RBSegment_file() (in module pyrosetta.rosetta.protocols.rbsegment_relax) read_RDC_file() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) read_resource_locators_tags() (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) read_resource_options_tags() (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) read_resources_tags() (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) read_ring_sizes_and_morphemes_from_database_file() (in module pyrosetta.rosetta.core.chemical.carbohydrates) read_score_headers() (pyrosetta.rosetta.core.io.silent.SilentStruct method) read_sequence() (pyrosetta.rosetta.core.io.silent.SilentStruct method) read_short_names_to_iupac_format_string() (in module pyrosetta.rosetta.core.chemical.carbohydrates) read_spine_x() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_ss2() (in module pyrosetta.rosetta.protocols.mpi_refinement) read_ss_file() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_ss_files() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_std_frags_from_cmd() (in module pyrosetta.rosetta.core.fragment) read_stream() (pyrosetta.rosetta.core.io.silent.SilentFileData method) read_structures() (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) read_tag() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) read_tags_fast() (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) read_talos_ss() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_topol_file() (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) read_topology_file() (in module pyrosetta.rosetta.core.chemical) read_vall() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_xfres_binary() (in module pyrosetta.rosetta.core.scoring.motif) ReadNativeRotamersFile (class in pyrosetta.rosetta.protocols.sewing) ReadRepeatNativeRotamersFile (class in pyrosetta.rosetta.protocols.sewing) ReadResfileAndObeyLengthEvents (class in pyrosetta.rosetta.core.pack.task.operation) readsome() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) readValueOrDie() (in module pyrosetta.rosetta.core.scoring.func) ready() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) ready_for_nonideal_scoring() (pyrosetta.rosetta.core.scoring.ScoreFunction method) ready_to_align() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) real2afteroption() (in module pyrosetta.rosetta.basic.options) Real2string() (in module pyrosetta.rosetta.utility) real3afteroption() (in module pyrosetta.rosetta.basic.options) real_regex_pattern() (in module pyrosetta.rosetta.utility.tag) real_to_virtual() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.pose.Pose method) realafteroption() (in module pyrosetta.rosetta.basic.options) RealAngleToShort() (in module pyrosetta.rosetta.protocols.loophash) RealFilter (class in pyrosetta.rosetta.core.chemical) RealOption (class in pyrosetta.rosetta.utility.options) RealOptionKey (class in pyrosetta.rosetta.utility.options) RealVectorOption (class in pyrosetta.rosetta.utility.options) RealVectorOptionKey (class in pyrosetta.rosetta.utility.options) reassign_atoms_for_intra_residue_stubs() (pyrosetta.rosetta.core.kinematics.FoldTree method) rebuild_disulfide() (in module pyrosetta.rosetta.core.util) rebuild_fa_disulfides() (in module pyrosetta.rosetta.core.util) rebuild_loops_until_closed() (in module pyrosetta.rosetta.protocols.comparative_modeling) rebuild_missing_atoms() (in module pyrosetta.rosetta.protocols.denovo_design) rebuild_pdb2pose() (pyrosetta.rosetta.core.pose.PDBInfo method) rebuild_polymer_bond_dependent_atoms() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) rebuild_polymer_bond_dependent_atoms_this_residue_only() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) rebuild_residue_connection_dependent_atoms() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) recalculate_rmsd_and_output_silent_file() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) recalculate_transforms() (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) recalculate_z_coordinate() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) recces_pose_setup() (in module pyrosetta.rosetta.protocols.recces) receive_char_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) receive_double_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) receive_doubles_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) receive_integer_from_anyone() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) receive_integer_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) receive_integers_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) receive_message() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) receive_observers_from() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) receive_size_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) receive_sizes_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) receive_string_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) recent_history_queue (class in pyrosetta.rosetta.utility) recenter() (in module pyrosetta.rosetta.core.conformation.symmetry) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) record() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) record_match() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) RecordCollection (class in pyrosetta.rosetta.core.io.pdb) RecordType (class in pyrosetta.rosetta.core.io.pdb) recover_checkpoint() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) recover_conformer_sidechains() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) recover_low() (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) recover_original_on_failure() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) recover_sidechains() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) recovery_rate() (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) recreate_task() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) recursive() (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) redefine_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) RedefineChi (class in pyrosetta.rosetta.core.chemical) redo() (pyrosetta.rosetta.protocols.jumping.SameStrand method) Reduced_Jdipolar() (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) reducible() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) ref() (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) ref_pose_for() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) reference() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) reference_copy() (pyrosetta.rosetta.ObjexxFCL.Dimension method) reference_name() (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) reference_pdb_id() (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation method) reference_pose() (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) reference_pose_cop() (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) reference_pose_from_current() (pyrosetta.rosetta.core.pose.Pose method) reference_pose_name() (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) reference_pose_set() (pyrosetta.rosetta.core.pose.Pose method) reference_pose_set_cop() (pyrosetta.rosetta.core.pose.Pose method) ReferencePose (class in pyrosetta.rosetta.core.pose.reference_pose) ReferencePoseSet (class in pyrosetta.rosetta.core.pose.reference_pose) refpose_enabled_residue_number_string() (in module pyrosetta.rosetta.utility.tag) refresh_bbstub_constraints() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) refresh_coordinate_constraints() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) refresh_energy_cache() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) refuse_unexpected_files() (pyrosetta.rosetta.utility.io.FileContentsMap method) regenerate_model() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) RegEx_based_CDR_Detector (class in pyrosetta.rosetta.protocols.antibody.grafting) RegExManager (class in pyrosetta.rosetta.protocols.antibody.grafting) region() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) region1() (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) region2() (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) region_all() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) region_simple() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) RegionalConnections (class in pyrosetta.rosetta.protocols.simple_filters) register_clash() (pyrosetta.rosetta.protocols.hbnet.HBondNode method) register_common_options() (in module pyrosetta.rosetta.protocols.abinitio) register_factory_prototypes() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) register_ff() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) register_options() (in module pyrosetta.rosetta.protocols.evaluation) (in module pyrosetta.rosetta.protocols.jd2) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.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.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.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.comparative_modeling.AlignRmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.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.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.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.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_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.simple_filters.CamShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.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.sparta.ChemicalShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator method) register_options_broker() (in module pyrosetta.rosetta.protocols.abinitio) register_options_universal_main() (in module pyrosetta.rosetta.protocols.jobdist) register_score_maker() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) register_variable_expression() (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) register_work_unit() (pyrosetta.rosetta.protocols.wum.WorkUnitList method) reindex_residues() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) reindex_sections() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) reinitialize() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) reinitialize_active_energy_methods() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) reinitialize_CCD_torsions() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) reinitialize_for_each_job() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.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.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.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.RemoveConstraints method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.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.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.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.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_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.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.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.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) reinitialize_for_new_input() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.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.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.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.RemoveConstraints method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.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.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.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.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_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.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.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.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) reinitialize_mingraph_neighborhood_for_residue() (in module pyrosetta.rosetta.core.pack) reinitialize_minnode_for_residue() (pyrosetta.rosetta.core.scoring.ScoreFunction method) reject_change() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) reject_mutant() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) rel_per_res_sc_sasa() (in module pyrosetta.rosetta.core.scoring.sasa) relative() (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) relative_pose_filter() (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids method) relative_pose_names() (pyrosetta.rosetta.protocols.simple_filters.Operator method) RelativeConnectRight (class in pyrosetta.rosetta.protocols.forge.build) RelativeSegmentFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) RelativeSequencePosition (class in pyrosetta.rosetta.protocols.forge.build) relax() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) relax_cdrs() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) relax_interface() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) Relax_main() (in module pyrosetta.rosetta.protocols.relax) relax_mover() (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) relax_optimized_CDR_grafts() (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) relax_pose() (in module pyrosetta.rosetta.protocols.relax) release_buffers() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) ReleaseConstraintFromResidueMover (class in pyrosetta.rosetta.protocols.fold_from_loops) remap() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) remap_allowed_residues_to_template() (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues method) remap_atom_vds() (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) remap_cis_omega_torsion_bins_to_trans() (in module pyrosetta.rosetta.core.conformation) remap_pdb_atom_names() (pyrosetta.rosetta.core.chemical.ResidueType method) remap_rb_segments() (in module pyrosetta.rosetta.protocols.rbsegment_relax) remap_resid() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) remap_residue() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) remap_residue_level_tasks() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) remap_residue_positions() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) remapped_clone() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) remarks() (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.pose.PDBInfo method) remember_unrecognized_res() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) remember_unrecognized_water() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) remodel_fold_tree_to_account_for_insertion() (in module pyrosetta.rosetta.core.kinematics) remodel_generic_taskfactory() (in module pyrosetta.rosetta.protocols.forge.methods) RemodelConstraintGenerator (class in pyrosetta.rosetta.protocols.forge.remodel) remodelData() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) RemodelLoopMover (class in pyrosetta.rosetta.protocols.forge.remodel) RemodelLoopMoverPoseFolder (class in pyrosetta.rosetta.protocols.denovo_design.components) remove() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) remove_all_anchors_and_ENF() (in module pyrosetta.rosetta.protocols.hydrate) remove_all_enzdes_constraints() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) remove_all_jump_atoms() (in module pyrosetta.rosetta.protocols.denovo_design) remove_all_variant_types() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) remove_all_virtual_phosphates() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) remove_and_store_bracketed() (in module pyrosetta.rosetta.core.pose.rna) remove_bad_inputs_from_job_list() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) remove_base_residue_type() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) remove_bracketed() (in module pyrosetta.rosetta.core.pose.rna) remove_carbohydrate_branch_point_variants() (in module pyrosetta.rosetta.core.pose.carbohydrates) remove_chain_break_jump_point() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) remove_chain_break_variants() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) remove_chainbreaks_according_to_jumps() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) remove_checkpoint_file() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) remove_connection_inconsistencies() (pyrosetta.rosetta.protocols.sewing.Hasher method) remove_constraint() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) remove_constraints() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) remove_constraints_of_type() (in module pyrosetta.rosetta.core.scoring.constraints) remove_coordinate_constraints_from_pose() (in module pyrosetta.rosetta.protocols.protein_interface_design) remove_covalent_connection_from_pose() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo method) remove_covalent_connections_from_pose() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) remove_cut() (in module pyrosetta.rosetta.protocols.jumping) remove_cutpoint() (in module pyrosetta.rosetta.protocols.forge.methods) remove_cutpoint_closed() (in module pyrosetta.rosetta.protocols.rna.denovo) remove_cutpoint_variants() (in module pyrosetta.rosetta.core.util) (in module pyrosetta.rosetta.protocols.forge.methods) (in module pyrosetta.rosetta.protocols.loops) remove_cutpoint_variants_for_ccd() (in module pyrosetta.rosetta.protocols.grafting) remove_cutpoints() (in module pyrosetta.rosetta.protocols.forge.methods) remove_cutpoints_closed() (in module pyrosetta.rosetta.protocols.rna.denovo) remove_duplicates() (pyrosetta.rosetta.protocols.sewing.Hasher method) remove_evaluation() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) remove_file() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) remove_high_energy_water_molecules() (in module pyrosetta.rosetta.protocols.hydrate) remove_hotspot_constraints_from_pose() (in module pyrosetta.rosetta.protocols.hotspot_hashing) remove_last_filter() (pyrosetta.rosetta.protocols.filters.FilterCollection method) remove_ligand_canonical_residues() (in module pyrosetta.rosetta.core.pose) remove_lower_terminus_type_from_conformation_residue() (in module pyrosetta.rosetta.core.conformation) remove_lower_terminus_type_from_pose_residue() (in module pyrosetta.rosetta.core.pose) remove_mg_bound_waters() (in module pyrosetta.rosetta.protocols.magnesium) remove_missing_density() (in module pyrosetta.rosetta.protocols.loops) remove_missing_jump_atoms() (in module pyrosetta.rosetta.protocols.denovo_design) remove_models_from_dssp() (in module pyrosetta.rosetta.protocols.sewing) remove_non_buried_wat() (in module pyrosetta.rosetta.protocols.hydrate) remove_non_protein_residues() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) remove_nonbb_constraints() (in module pyrosetta.rosetta.core.scoring.constraints) remove_nonprotein_residues() (in module pyrosetta.rosetta.core.pose) remove_observer() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) remove_option() (pyrosetta.rosetta.basic.resource_manager.JobOptions method) remove_other_pose_at_idx() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) remove_register_shifts() (in module pyrosetta.rosetta.protocols.fldsgn.filters) remove_remark_header_for_geomcst() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) remove_remodel_constraints_from_pose() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) remove_short_chunks() (in module pyrosetta.rosetta.protocols.loops) remove_silent_file_if_it_exists() (in module pyrosetta.rosetta.core.io.silent) remove_singletons_and_update_pose_focus() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) remove_small_gaps() (in module pyrosetta.rosetta.protocols.loops) remove_terminal_loops() (pyrosetta.rosetta.protocols.loops.Loops method) remove_terminal_phosphates() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) remove_trigger() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) remove_unpatchable_residue_type() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) remove_upper_terminus_type_from_conformation_residue() (in module pyrosetta.rosetta.core.conformation) remove_upper_terminus_type_from_pose_residue() (in module pyrosetta.rosetta.core.pose) remove_variant_type() (pyrosetta.rosetta.core.chemical.ResidueType method) remove_variant_type_from_conformation_residue() (in module pyrosetta.rosetta.core.conformation) remove_variant_type_from_pose_residue() (in module pyrosetta.rosetta.core.pose) remove_variant_type_from_residue() (in module pyrosetta.rosetta.core.pose) remove_virtual_O2Prime_hydrogen() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) remove_virtual_residues() (in module pyrosetta.rosetta.core.pose) remove_virtual_rna_residue_variant_type() (in module pyrosetta.rosetta.core.pose.rna) remove_waters_except_mg_bound() (in module pyrosetta.rosetta.protocols.magnesium) RemoveConstraints (class in pyrosetta.rosetta.protocols.constraint_generator) RemoveHybridization() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) RemoveNorCTermMPM (class in pyrosetta.rosetta.protocols.match) RemoveRotamerSpecifications (class in pyrosetta.rosetta.core.chemical) rename_atom() (pyrosetta.rosetta.core.io.ResidueInformation method) rename_atoms() (in module pyrosetta.rosetta.core.chemical) rename_energies() (pyrosetta.rosetta.core.io.silent.SilentStruct method) renormalize_quota_pools() (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) renormalize_weights() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) renumber_after_variant_changes() (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap method) renumber_all_decoys() (pyrosetta.rosetta.core.io.silent.SilentFileData method) renumber_jumps() (pyrosetta.rosetta.core.kinematics.FoldTree method) renumber_jumps_ordered() (pyrosetta.rosetta.core.kinematics.FoldTree method) renumber_pdb() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) renumber_pdbinfo_based_on_conf_chains() (in module pyrosetta.rosetta.core.pose) renumber_rotamers() (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) renumber_with_pdb_info() (in module pyrosetta.rosetta.protocols.hybridization) reorder() (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) reorder_foldtree_around_mobile_regions() (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) reorder_full_model_info_after_append() (in module pyrosetta.rosetta.core.pose.full_model_info) reorder_full_model_info_after_delete() (in module pyrosetta.rosetta.core.pose.full_model_info) reorder_full_model_info_after_prepend() (in module pyrosetta.rosetta.core.pose.full_model_info) reorder_glycan_residues() (in module pyrosetta.rosetta.core.io) reorder_membrane_foldtree() (in module pyrosetta.rosetta.protocols.membrane) reorder_pose() (in module pyrosetta.rosetta.core.import_pose) reorder_randomly() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) reorder_root_partition_res() (in module pyrosetta.rosetta.core.pose) reorder_with_first_non_mobile_as_root() (in module pyrosetta.rosetta.protocols.ligand_docking) reorient_extended_fibril() (in module pyrosetta.rosetta.protocols.fibril) rep_weight() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) repack() (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker method) repack_antibody_interface() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) repack_antigen_ab_interface() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) repack_antigen_interface() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) repack_cdrs() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) repack_chain1() (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) repack_chain2() (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) repack_connection_and_residues_in_movemap() (in module pyrosetta.rosetta.protocols.grafting) repack_connection_and_residues_in_movemap_and_piece() (in module pyrosetta.rosetta.protocols.grafting) repack_connection_and_residues_in_movemap_and_piece_and_neighbors() (in module pyrosetta.rosetta.protocols.grafting) repack_shell() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation method) repackable_residues() (in module pyrosetta.rosetta.core.pack) repacking_residues() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) RepackingRefiner (class in pyrosetta.rosetta.protocols.loop_modeling.refiners) RepackLigandSiteWithoutLigandMover (class in pyrosetta.rosetta.protocols.enzdes) RepackMinimize (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) RepackSidechainsMover (class in pyrosetta.rosetta.protocols.simple_moves) RepackTrialCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) repeat() (in module pyrosetta.rosetta.ObjexxFCL.format) repeat_generation_with_additional_residue() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) repeat_propagation() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) repeat_sync() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) repeat_to_preserve() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) repeating_unit_offset() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) RepeatMover (class in pyrosetta.rosetta.protocols.moves) repeats() (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) replace() (in module pyrosetta.rosetta.protocols.forge.methods) replace_atom() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) replace_conformation_residue_copying_existing_coordinates() (in module pyrosetta.rosetta.core.conformation) replace_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) replace_environment_variables() (in module pyrosetta.rosetta.utility) replace_file() (in module pyrosetta.rosetta.protocols.simple_moves) replace_in() (in module pyrosetta.rosetta.utility) replace_option_namespace_colons_with_underscores() (in module pyrosetta.rosetta.basic.options) replace_pose_residue_copying_existing_coordinates() (in module pyrosetta.rosetta.core.pose) replace_region() (in module pyrosetta.rosetta.protocols.grafting) replace_res() (pyrosetta.rosetta.core.pose.PDBInfo method) replace_res_remap_bfactors() (pyrosetta.rosetta.core.pose.PDBInfo method) replace_residue() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) replace_residue_in_atom_tree() (in module pyrosetta.rosetta.core.conformation) replace_residue_keeping_all_atom_positions() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) replace_spaces() (in module pyrosetta.rosetta.utility) replace_tree() (pyrosetta.rosetta.core.kinematics.AtomTree method) replaced_symmetric_foldtree_with_new_monomer() (in module pyrosetta.rosetta.core.conformation.symmetry) ReplaceMainchainAtom (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithBromine (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithChlorine (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithEthyl (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithFluorine (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithHydroxyl (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithIodine (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithMethoxy (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithMethyl (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithTrifluoromethyl (class in pyrosetta.rosetta.core.chemical) ReplaceRegionMover (class in pyrosetta.rosetta.protocols.grafting.simple_movers) replaces() (pyrosetta.rosetta.core.chemical.Patch method) replaces_residue_type() (pyrosetta.rosetta.core.chemical.Patch method) Report (class in pyrosetta.rosetta.basic) report() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.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.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) report_ab_H3_kink_metrics_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) report_ab_metrics_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) report_adducts() (pyrosetta.rosetta.core.chemical.ResidueType method) report_all_interface_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) report_batch_inconsistency() (in module pyrosetta.rosetta.protocols.jd2.archive) report_binary_stats() (pyrosetta.rosetta.protocols.sewing.SewGraph method) report_CA_rmsd() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) report_cdr_metrics_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) report_cdr_residue_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) report_cdr_residue_features_row() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) report_crd() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) report_data() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) report_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) report_heading_directions_of_all_AA_in_a_strand() (in module pyrosetta.rosetta.protocols.features.strand_assembly) report_interface_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) report_interface_residue_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) report_interface_side_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) report_property() (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) report_rotamer_recovery() (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) report_sm() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.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.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) report_subvalues() (pyrosetta.rosetta.protocols.simple_filters.Operator method) ReportEffectivePKA (class in pyrosetta.rosetta.protocols.simple_moves) Reporter (class in pyrosetta.rosetta.basic) ReportFSC (class in pyrosetta.rosetta.protocols.electron_density) ReportSequenceDifferences (class in pyrosetta.rosetta.protocols.protein_interface_design) representative_downstream_algorithm() (pyrosetta.rosetta.protocols.match.Matcher method) representative_group_matches() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) RepulsiveOnlyMover (class in pyrosetta.rosetta.protocols.simple_moves) request_data_from_head_node() (in module pyrosetta.rosetta.basic.mpi) request_fold_tree() (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) request_symmetrize_by_intersection() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) request_symmetrize_by_union() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) require_all_target_residue_atom_coordinates() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) require_candidate_residue_atoms_to_lie_near_target_atom() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) require_context_graph() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) require_final() (pyrosetta.rosetta.core.chemical.ResidueType method) require_mm_bend() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) require_target_atom_coordinate() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) required_attribute() (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) required_name_attribute() (in module pyrosetta.rosetta.utility.tag) RequirementFactory (class in pyrosetta.rosetta.protocols.sewing.sampling.requirements) requires_a_setup_for_derivatives_for_residue_opportunity() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) requires_a_setup_for_derivatives_for_residue_pair_opportunity() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) requires_a_setup_for_scoring_for_residue_opportunity_during_minimization() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) requires_a_setup_for_scoring_for_residue_pair_opportunity() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method)

requires_actcoord() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) requires_context_graph() (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) requires_pose() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) reroot() (in module pyrosetta.rosetta.core.pose) reroot_based_on_full_model_info() (in module pyrosetta.rosetta.protocols.stepwise.modeler) res() (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) res1() (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.RDC method) res2() (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.RDC method) res3() (pyrosetta.rosetta.core.scoring.CSA method) res_filter_schema_w_attributes() (in module pyrosetta.rosetta.core.pack.task.operation) res_haslabel() (pyrosetta.rosetta.core.pose.PDBInfo method) res_ids() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) res_in_chain() (in module pyrosetta.rosetta.core.pose) res_is_mirrored() (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) res_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) res_lvl_task_op_schema_empty() (in module pyrosetta.rosetta.core.pack.task.operation) res_lvl_task_op_schema_w_attributes() (in module pyrosetta.rosetta.core.pack.task.operation) res_min_data() (pyrosetta.rosetta.core.scoring.MinimizationNode method) res_moved() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) res_name() (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) res_name1() (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) res_name2() (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) res_num() (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) res_pair_min_data() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) res_res_min_distance() (in module pyrosetta.rosetta.protocols.simple_filters) res_res_weight() (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer method) res_rmsd() (in module pyrosetta.rosetta.protocols.protein_interface_design.filters) res_selector_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader method) resA() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) resB() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) rescale_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) ResConnID (class in pyrosetta.rosetta.core.chemical) rescore() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) reserve() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) reserve_buffers() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) reserve_destination_size() (pyrosetta.rosetta.utility.subset_mapping method) reservoir_sample_accept_prob() (in module pyrosetta.rosetta.numeric.random) RESET (class in pyrosetta.rosetta.core.pack.task) reset() (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) Reset() (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) reset() (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.checkpoint.Timer method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) reset_3d_projection() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) reset_accept_counter() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) reset_accounting() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) reset_arrays_danger_expert_only() (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase method) reset_base_type_cop() (pyrosetta.rosetta.core.chemical.ResidueType method) reset_baseline() (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.simple_filters.Operator method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) reset_baselines() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) reset_bond_distance_to_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) reset_chain_endings() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) reset_count() (pyrosetta.rosetta.protocols.contact_map.Contact method) reset_counters() (pyrosetta.rosetta.protocols.moves.MonteCarlo method) reset_counts() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) reset_cycle_index() (pyrosetta.rosetta.protocols.moves.CycleMover method) reset_delta_omega1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) reset_delta_z1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) reset_edge_list_iterator_for_node() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) reset_energy_methods() (pyrosetta.rosetta.core.scoring.ScoreFunction method) reset_filters() (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) reset_jump_rb_deltas() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) reset_mainchain_torsion_potential_names() (pyrosetta.rosetta.core.chemical.ResidueType method) reset_mode() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) reset_move_data() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) reset_nblist() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) reset_num_connections() (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) reset_r1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) reset_recovery() (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) reset_res_moved() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) reset_residue_list() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) reset_residue_type_set_for_conf() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) reset_rpe_calculations_count() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) reset_sample_index() (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation method) reset_scorefxn() (pyrosetta.rosetta.protocols.moves.MonteCarlo method) reset_status() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.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.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.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.RemoveConstraints method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.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.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.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.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_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.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.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.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) reset_structure_moved() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) reset_surface_residue_information() (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) reset_task_factory() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) reset_x() (in module pyrosetta.rosetta.protocols.toolbox) ResetBondLength (class in pyrosetta.rosetta.core.chemical) resfile() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) resfile_commands() (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) ResfileCommand (class in pyrosetta.rosetta.core.pack.task) ResFilterCreator (class in pyrosetta.rosetta.core.pack.task.operation) ResHasher (class in pyrosetta.rosetta.protocols.mean_field) ResHashMap (class in pyrosetta.rosetta.protocols.mean_field) resi() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) ResId (class in pyrosetta.rosetta.protocols.moves) resid() (pyrosetta.rosetta.core.chemical.ResConnID method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation method) residual_squared_of_points_to_plane() (in module pyrosetta.rosetta.numeric.geometry) ResidualDipolarCoupling (class in pyrosetta.rosetta.core.scoring) ResidualDipolarCouplingRigidSegments (class in pyrosetta.rosetta.protocols.scoring) Residue (class in pyrosetta.rosetta.core.conformation) (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover) residue() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc method) (pyrosetta.rosetta.core.scoring.func.XYZ_Func method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) residue_action() (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.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.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.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) residue_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) residue_atomtree_collection() (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection method) residue_atomtree_collection_op() (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection method) residue_base2_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) residue_base_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) residue_center_of_mass() (in module pyrosetta.rosetta.core.conformation.symmetry) (in module pyrosetta.rosetta.core.pose) residue_conformations_redundant() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) residue_connect_atom_index() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) residue_connection() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) residue_connection_conn_id() (pyrosetta.rosetta.core.conformation.Residue method) residue_connection_id_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) residue_connection_is_polymeric() (pyrosetta.rosetta.core.chemical.ResidueType method) residue_connection_partner() (pyrosetta.rosetta.core.conformation.Residue method) residue_connections_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) residue_cop() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) residue_data() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) residue_energy() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) residue_energy_ext() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) residue_gws_string() (in module pyrosetta.rosetta.core.io.carbohydrates) residue_hbonds() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) residue_index() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) residue_info() (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) residue_is_floppy() (in module pyrosetta.rosetta.protocols.sic_dock) residue_is_in_fold_tree() (pyrosetta.rosetta.core.kinematics.FoldTree method) residue_is_surface() (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) residue_iterated_on() (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) residue_list() (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) residue_near_water() (in module pyrosetta.rosetta.core.scoring.hbonds) (in module pyrosetta.rosetta.protocols.hydrate) residue_neighbors_updated() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) residue_num() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) residue_number_string() (in module pyrosetta.rosetta.utility.tag) residue_numbers_into_pose() (pyrosetta.rosetta.core.io.silent.SilentStruct method) residue_packed() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) residue_packer_states() (in module pyrosetta.rosetta.protocols.rosetta_scripts) residue_pair_constraint_exists() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) residue_pair_constraints_begin() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) residue_pair_constraints_end() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) residue_pair_constraints_exists() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) residue_pair_energy() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) residue_pair_energy_ext() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) residue_point_graph_from_conformation() (in module pyrosetta.rosetta.core.conformation) residue_range_gws_string() (in module pyrosetta.rosetta.core.io.carbohydrates) residue_rotamer_recovery() (in module pyrosetta.rosetta.core.pack) residue_sc_rmsd_no_super() (in module pyrosetta.rosetta.core.scoring) (in module pyrosetta.rosetta.protocols.hotspot_hashing) residue_selector() (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) residue_selector_single_from_line() (in module pyrosetta.rosetta.core.chemical) residue_subset() (in module pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators) residue_task() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) residue_total_energies() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) residue_total_energy() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) residue_type() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) residue_type_all_patches_name() (in module pyrosetta.rosetta.core.chemical) residue_type_base_name() (in module pyrosetta.rosetta.core.chemical) residue_type_base_names() (pyrosetta.rosetta.core.io.StructFileRep method) residue_type_ptr() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) residue_type_set() (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) residue_type_set_for_conf() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) residue_type_set_for_pose() (pyrosetta.rosetta.core.pose.Pose method) residue_type_set_mode() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) residue_types_from_saccharide_sequence() (in module pyrosetta.rosetta.core.pose) residue_types_from_sequence() (in module pyrosetta.rosetta.core.pose) residue_typeset_mode() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) residue_xyz_change_list_begin() (pyrosetta.rosetta.core.kinematics.AtomTree method) residue_xyz_change_list_end() (pyrosetta.rosetta.core.kinematics.AtomTree method) residue_z_position() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) ResidueAtomTreeCollection (class in pyrosetta.rosetta.core.pack.scmin) ResidueAtomTreeCollectionMomento (class in pyrosetta.rosetta.core.pack.scmin) ResidueBurialFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueChainVectorOption (class in pyrosetta.rosetta.utility.options) ResidueChainVectorOptionKey (class in pyrosetta.rosetta.utility.options) ResidueConformationFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueConformerFilter (class in pyrosetta.rosetta.protocols.enzdes) ResidueConnection (class in pyrosetta.rosetta.core.chemical) ResidueConstraints (class in pyrosetta.rosetta.core.scoring.constraints) ResidueCoordinateChangeList (class in pyrosetta.rosetta.core.kinematics) ResidueDepthCalculator (class in pyrosetta.rosetta.protocols.simple_filters) ResidueDepthData (class in pyrosetta.rosetta.protocols.simple_filters) ResidueDepthFilter (class in pyrosetta.rosetta.protocols.simple_filters) ResidueElement (class in pyrosetta.rosetta.protocols.environment.claims) ResidueFactory (class in pyrosetta.rosetta.core.conformation) ResidueFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueGridScoresFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueHasProperty (class in pyrosetta.rosetta.core.pack.task.operation) ResidueIdentifier (class in pyrosetta.rosetta.protocols.loops) ResidueIndexDescription (class in pyrosetta.rosetta.core.pose) ResidueIndexDescriptionFromFile (class in pyrosetta.rosetta.core.pose) ResidueIndexSelector (class in pyrosetta.rosetta.core.select.residue_selector) ResidueInformation (class in pyrosetta.rosetta.core.io) ResidueLevelTask_ (class in pyrosetta.rosetta.core.pack.task) ResidueNameSelector (class in pyrosetta.rosetta.core.select.residue_selector) ResidueNetwork (class in pyrosetta.rosetta.protocols.toolbox) ResiduePairJumpSetup (class in pyrosetta.rosetta.protocols.jumping) ResiduePairJumpSingle (class in pyrosetta.rosetta.protocols.jumping) ResiduePDBInfoHasLabelSelector (class in pyrosetta.rosetta.core.select.residue_selector) ResidueProbDesignOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) ResidueProperties (class in pyrosetta.rosetta.core.chemical) ResidueProperty (class in pyrosetta.rosetta.core.chemical) ResidueRange (class in pyrosetta.rosetta.core.select.residue_selector) residues() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) residues_downstream_of_jump() (in module pyrosetta.rosetta.core.kinematics) residues_for_atom_name_remapping() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) residues_interact() (in module pyrosetta.rosetta.core.scoring.methods) residues_moved_begin() (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) residues_moved_end() (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) residues_per_repeat() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) residues_upstream_of_jump() (in module pyrosetta.rosetta.core.kinematics) ResidueScoresFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueSecondaryStructureFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueSelectorLoader (class in pyrosetta.rosetta.protocols.parser) ResidueSpanSelector (class in pyrosetta.rosetta.core.select.residue_selector) ResidueTorsionRestraints (class in pyrosetta.rosetta.protocols.ligand_docking) ResidueTotalScoresFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueType (class in pyrosetta.rosetta.core.chemical) residueType() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) ResidueTypeConstraint (class in pyrosetta.rosetta.core.scoring.constraints) ResidueTypeConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) ResidueTypeLinkingConstraint (class in pyrosetta.rosetta.core.scoring.constraints) ResidueTypeSelector (class in pyrosetta.rosetta.core.chemical) ResidueTypeSelectorSingle (class in pyrosetta.rosetta.core.chemical) ResidueTypeSet (class in pyrosetta.rosetta.core.chemical) ResidueTypesFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueVicinityInfo (class in pyrosetta.rosetta.protocols.forge.remodel) ResidueVicinityRCG (class in pyrosetta.rosetta.protocols.forge.remodel) resindex() (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) resize() (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.core.scoring.Helices method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.Strands method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) resize_atom_records() (pyrosetta.rosetta.core.pose.PDBInfo method) resize_bb_donor_acceptor_arrays() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) resize_residue_records() (pyrosetta.rosetta.core.pose.PDBInfo method) ResLvlTaskOperationCreator (class in pyrosetta.rosetta.core.pack.task.operation) resName() (pyrosetta.rosetta.core.io.ResidueInformation method) resname() (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) resnum() (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) resnum_and_chain() (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) resnum_exists_in_set() (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation method) resolution() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) resolve_db_partition() (in module pyrosetta.rosetta.basic.database) resolve_index() (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) resolve_loop_indices() (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) resolve_loop_indices_once() (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) Resonance (class in pyrosetta.rosetta.protocols.noesy_assign) resonance() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) resonance_id() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) ResonanceList (class in pyrosetta.rosetta.protocols.noesy_assign) resonances() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) resonances_at_residue() (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) resource_description() (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator method) ResourceConfiguration (class in pyrosetta.rosetta.basic.resource_manager) ResourceLoader (class in pyrosetta.rosetta.basic.resource_manager) ResourceLoaderCreator (class in pyrosetta.rosetta.basic.resource_manager) ResourceLoaderFactory (class in pyrosetta.rosetta.basic.resource_manager) ResourceLocator (class in pyrosetta.rosetta.basic.resource_manager) ResourceLocatorCreator (class in pyrosetta.rosetta.basic.resource_manager) ResourceLocatorFactory (class in pyrosetta.rosetta.basic.resource_manager) ResourceManager (class in pyrosetta.rosetta.basic.resource_manager) ResourceManagerCreator (class in pyrosetta.rosetta.basic.resource_manager) ResourceManagerFactory (class in pyrosetta.rosetta.basic.resource_manager) ResourceOptions (class in pyrosetta.rosetta.basic.resource_manager) ResourceOptionsCreator (class in pyrosetta.rosetta.basic.resource_manager) ResourceOptionsFactory (class in pyrosetta.rosetta.basic.resource_manager) ResourceStream (class in pyrosetta.rosetta.basic.resource_manager) respect_this_movemap() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) respond_to_peripheral_hitlist_change() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) respond_to_primary_hitlist_change() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) ResPred (class in pyrosetta.rosetta.protocols.mean_field) ResRangePredicate (class in pyrosetta.rosetta.core.scoring) resSeq() (pyrosetta.rosetta.core.io.ResidueInformation method) restart() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) restart_mode() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) restart_simulation() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) restore() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) restore_archive() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) restore_from_file() (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) restore_pose_from_rbsegs() (in module pyrosetta.rosetta.protocols.rbsegment_relax) restore_residues() (in module pyrosetta.rosetta.protocols.forge.methods) restore_status() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) restoreState() (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) restrain_ligand_nbr_atom() (in module pyrosetta.rosetta.protocols.ligand_docking) restrain_protein_Calphas() (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) restrict_absent_canonical_aas() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) restrict_absent_nas() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) restrict_access() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) restrict_identities() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) restrict_non_nbrs_from_repacking() (in module pyrosetta.toolbox) restrict_nonnative_canonical_aas() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) restrict_only_design_to_loops() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors method) restrict_prec() (in module pyrosetta.rosetta.core.io.pose_to_sfr) restrict_sequence_profile() (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) restrict_to_aligned_segments() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) restrict_to_canonical_aas() (in module pyrosetta.rosetta.protocols.multistate_design) restrict_to_protein_residues() (in module pyrosetta.rosetta.protocols.ligand_docking) restrict_to_repacking() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) restrict_to_residue() (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) restrict_to_residues() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) restrict_to_single_sequence() (in module pyrosetta.rosetta.protocols.dna) RestrictByCalculatorsOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) RestrictChainToRepackingOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) RestrictConservedLowDdgOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) RestrictIdentitiesAtAlignedPositionsOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) RestrictIdentitiesOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) restriction_type_name() (in module pyrosetta.rosetta.utility.tag) RestrictNonSurfaceToRepackingOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) RestrictOperationsBase (class in pyrosetta.rosetta.protocols.toolbox.task_operations) RestrictResiduesToRepackingOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) RestrictResidueToRepacking (class in pyrosetta.rosetta.core.pack.task.operation) RestrictToAlignedSegmentsOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) RestrictToCDRsAndNeighbors (class in pyrosetta.rosetta.protocols.antibody.task_operations) RestrictToInterfaceOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) RestrictToInterfaceVectorOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) RestrictToLoopsAndNeighbors (class in pyrosetta.rosetta.protocols.toolbox.task_operations) RestrictToMoveMapChiOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) RestrictToNeighborhoodOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) RestrictYSDesign (class in pyrosetta.rosetta.core.pack.task.operation) restype() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) restype_char() (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) restype_destruction_observer() (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap method) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) restype_geometry() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) restype_index() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) RestypeDestructionEvent (class in pyrosetta.rosetta.core.chemical) restypeinfo() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) result_sizes() (in module pyrosetta.rosetta.protocols.antibody.grafting) retain_top() (in module pyrosetta.rosetta.core.fragment) retrieve_base_partner_from_pose() (in module pyrosetta.rosetta.core.scoring.dna) retrieve_bulges() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) retrieve_bulges_s() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) retrieve_centroid_scatter_from_pose() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) retrieve_connection_architect() (in module pyrosetta.rosetta.protocols.denovo_design.connection) retrieve_constraints() (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) retrieve_CSA_from_pose() (in module pyrosetta.rosetta.core.scoring) retrieve_DC_from_pose() (in module pyrosetta.rosetta.core.scoring) retrieve_denovo_architect() (in module pyrosetta.rosetta.protocols.denovo_design.architects) retrieve_energy() (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) retrieve_fa_scatter_from_pose() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) retrieve_lengths() (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) retrieve_observer() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) retrieve_RDC_from_pose() (in module pyrosetta.rosetta.core.scoring) retrieve_RDC_ROHL_from_pose() (in module pyrosetta.rosetta.core.scoring) retrieve_RDC_segments_from_pose() (in module pyrosetta.rosetta.protocols.scoring) retrieve_register_shifts() (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) retrieve_residue_num_of_rkde() (in module pyrosetta.rosetta.protocols.features.strand_assembly) RetrieveStoredTaskOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) return_centroid() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) return_hbond_to_queue() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) return_key() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) return_nearest_residue() (in module pyrosetta.rosetta.core.conformation.symmetry) (in module pyrosetta.rosetta.core.pose) return_region() (in module pyrosetta.rosetta.protocols.grafting) ReturnResidueSubsetSelector (class in pyrosetta.rosetta.core.select.residue_selector) ReturnSidechainMover (class in pyrosetta.rosetta.protocols.simple_moves) reverse() (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) reverse_chains() (in module pyrosetta.rosetta.protocols.denovo_design.components) reverse_connections() (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) reverse_lengths() (in module pyrosetta.rosetta.protocols.denovo_design.components) reverse_orientations() (in module pyrosetta.rosetta.protocols.denovo_design.components) reverse_score_filter() (pyrosetta.rosetta.core.io.silent.SilentFileData method) reversed() (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.kinematics.Jump method) Revert (class in pyrosetta.rosetta.protocols.protein_interface_design) revert_to_pre_talaris_2013_defaults() (in module pyrosetta.rosetta.core.init) revise_root_and_moving_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) revise_root_and_moving_res_list() (in module pyrosetta.rosetta.protocols.stepwise.modeler) revision_id() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) reweighters_begin() (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer method) reweighters_end() (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer method) rg() (in module pyrosetta.rosetta.numeric.random) rgb_to_hsv() (in module pyrosetta.rosetta.numeric) right_justified() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) right_justify() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) right_string_of() (in module pyrosetta.rosetta.ObjexxFCL) right_stub_atoms() (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) rigid_transform_3D() (in module pyrosetta.toolbox.numpy_utils) RigidBodyDofPerturbMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyDofRandomizeMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyDofRandomTransMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyDofSeqPerturbMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyDofSeqRandomizeMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyDofSeqTransMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyDofTransMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyMoveBaseRSO (class in pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations) RigidBodyMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyMoveRSO (class in pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations) RigidBodyPerturbMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyPerturbNoCenterMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodySilentStructCreator (class in pyrosetta.rosetta.core.io.silent) RigidBodySpinMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyTiltMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyTransMover (class in pyrosetta.rosetta.protocols.rigid) RigidChunkClaimer (class in pyrosetta.rosetta.protocols.topology_broker) RigidSearchMover (class in pyrosetta.rosetta.protocols.ligand_docking) ring_affix_from_ring_size() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) ring_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) ring_conformer() (pyrosetta.rosetta.core.conformation.Residue method) ring_conformer_set() (pyrosetta.rosetta.core.chemical.ResidueType method) ring_current_coeff() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) ring_current_effect() (in module pyrosetta.rosetta.core.scoring.rna.chemical_shift) ring_height() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) ring_intensity() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) ring_pos() (in module pyrosetta.rosetta.core.scoring.rna.chemical_shift) ring_radius() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) RingConformationMover (class in pyrosetta.rosetta.protocols.simple_moves) RingConformationMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) RingConformer (class in pyrosetta.rosetta.core.chemical.rings) RingConformerManager (class in pyrosetta.rosetta.core.chemical.rings) ringness() (pyrosetta.rosetta.core.chemical.Bond method) rjust() (in module pyrosetta.rosetta.ObjexxFCL) rKirkwood() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) rm_virt_phosphate() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) rms_at_all_corresponding_atoms() (in module pyrosetta.rosetta.core.scoring) rms_at_corresponding_atoms() (in module pyrosetta.rosetta.core.scoring) rms_at_corresponding_atoms_no_super() (in module pyrosetta.rosetta.core.scoring) rms_at_corresponding_heavy_atoms() (in module pyrosetta.rosetta.core.scoring) rms_error_with_noise() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) rms_fit() (in module pyrosetta.rosetta.numeric.model_quality) rms_pose_list() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) rms_wrapper() (in module pyrosetta.rosetta.numeric.model_quality) rms_wrapper_slow_and_correct() (in module pyrosetta.rosetta.numeric.model_quality) RMSD() (in module pyrosetta.rosetta.protocols.cluster.calibur) rmsd() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) rmsd_over_residue_list() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) rmsd_screen() (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) RmsData (class in pyrosetta.rosetta.numeric.model_quality) RmsdEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) RMSDReporter (class in pyrosetta.rosetta.protocols.pose_reporters) RmsdTargetEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) rmsfitca3() (in module pyrosetta.rosetta.numeric.model_quality) RMSwrapper() (in module pyrosetta.rosetta.protocols.simple_filters) RNA_AddDeleteMonteCarlo (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna) RNA_AnalyticLoopCloser (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) rna_anti_chi_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) rna_backbone_backbone_pair_energy() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) RNA_base_atoms() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) rna_base_backbone_pair_energy() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) rna_block_stack_above_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) rna_block_stack_below_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) rna_bulge_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) rna_centroid_info() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) RNA_CentroidInfo (class in pyrosetta.rosetta.core.scoring.rna) RNA_ChemicalShiftEnergy (class in pyrosetta.rosetta.core.scoring.rna.chemical_shift) RNA_ChunkLibrary (class in pyrosetta.rosetta.protocols.rna.denovo.libraries) RNA_CS_parameters (class in pyrosetta.rosetta.core.scoring.rna.chemical_shift) RNA_CS_residue_parameters (class in pyrosetta.rosetta.core.scoring.rna.chemical_shift) rna_data() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) rna_data_info() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) RNA_DataInfo (class in pyrosetta.rosetta.core.pose.rna) RNA_DataReader (class in pyrosetta.rosetta.core.io.rna) RNA_DeNovoPoseInitializer (class in pyrosetta.rosetta.protocols.rna.denovo.setup) RNA_DeNovoProtocol (class in pyrosetta.rosetta.protocols.rna.denovo) rna_dna_match() (in module pyrosetta.rosetta.core.chemical.rna) rna_filtered_base_base_info() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) RNA_FilteredBaseBaseInfo (class in pyrosetta.rosetta.core.pose.rna) RNA_FittedTorsionInfo (class in pyrosetta.rosetta.core.chemical.rna) rna_fragment_library() (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager method) rna_fragment_monte_carlo() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) RNA_FragmentMover (class in pyrosetta.rosetta.protocols.rna.denovo.movers) RNA_HelixAssembler (class in pyrosetta.rosetta.protocols.rna.movers) RNA_Info (class in pyrosetta.rosetta.core.chemical.rna) RNA_info() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) rna_jump_library() (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager method) rna_jump_library_cop() (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager method) RNA_JumpLibrary (class in pyrosetta.rosetta.protocols.rna.denovo.libraries) RNA_KinematicCloser (class in pyrosetta.rosetta.protocols.stepwise.sampler.rna) rna_legacy_output_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) RNA_LibraryManager (class in pyrosetta.rosetta.protocols.rna.denovo.libraries) RNA_LoopCloser (class in pyrosetta.rosetta.protocols.rna.movers) RNA_LowResolutionPotential (class in pyrosetta.rosetta.core.scoring.rna) RNA_Minimizer (class in pyrosetta.rosetta.protocols.rna.denovo.movers) RNA_O2PrimeMover (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna) rna_options() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) RNA_PairingTemplate (class in pyrosetta.rosetta.protocols.rna.denovo.libraries) rna_params() (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer method) rna_raw_base_base_info() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) RNA_RawBaseBaseInfo (class in pyrosetta.rosetta.core.pose.rna) rna_reactivities() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) RNA_Relaxer (class in pyrosetta.rosetta.protocols.rna.denovo.movers) rna_repulsive_pair_energy() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) rna_residue_name_to_num() (in module pyrosetta.rosetta.core.scoring.rna) rna_sample_sugar_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) rna_scoring_info_from_pose() (in module pyrosetta.rosetta.core.scoring.rna) RNA_ScoringInfo (class in pyrosetta.rosetta.core.scoring.rna) RNA_SecStructLegacyInfo (class in pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy) RNA_SilentStructCreator (class in pyrosetta.rosetta.core.io.silent) RNA_SuiteAssignment (class in pyrosetta.rosetta.core.pose.rna) RNA_SuiteInfo (class in pyrosetta.rosetta.core.pose.rna) RNA_SuiteName (class in pyrosetta.rosetta.core.pose.rna) rna_syn_chi_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) rna_task() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) rna_terminal_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) RNA_TorsionMover (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna) rna_update_last_controlling_chi() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) RNAIdealizeMover (class in pyrosetta.rosetta.protocols.rna.movers) RNAThreadAndMinimizeMover (class in pyrosetta.rosetta.protocols.rna.movers) rnl_pose() (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) RNP_LowResPotential (class in pyrosetta.rosetta.core.scoring.rna) rolling_score() (in module pyrosetta.rosetta.protocols.frag_picker.scores) root() (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) root_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) root_expression() (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) root_from_code() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) rootj() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) rosetta_names_from_pdb_code() (pyrosetta.rosetta.core.io.NomenclatureManager method) rosetta_recharge_fullatom() (in module pyrosetta.rosetta.core.chemical) rosetta_res_type() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) rosetta_resName() (pyrosetta.rosetta.core.io.ResidueInformation method) rosetta_retype_fullatom() (in module pyrosetta.rosetta.core.chemical) rosetta_scripts_complex_type_naming_func() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) rosetta_scripts_element_name() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) RosettaModuleOptionType (class in pyrosetta.rosetta.utility.xsd_util) RosettaModuleType (class in pyrosetta.rosetta.utility.xsd_util) RosettaScriptsParser (class in pyrosetta.rosetta.protocols.rosetta_scripts) rot_center() (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) rot_ind() (pyrosetta.rosetta.protocols.mean_field.RotProb method) rot_magnitude() (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) rot_matrices() (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) rot_matrix() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) rot_pose() (in module pyrosetta.rosetta.protocols.sic_dock) rot_sample_from_name() (in module pyrosetta.rosetta.core.pack.task) rotamer() (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) rotamer_aa() (pyrosetta.rosetta.core.chemical.ResidueType method) rotamer_couplings() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) rotamer_couplings_exist() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) rotamer_data_cache() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) rotamer_energy() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) rotamer_energy_deriv() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) rotamer_from_chi() (in module pyrosetta.rosetta.core.pack.dunbrack) rotamer_from_chi_02() (in module pyrosetta.rosetta.core.pack.dunbrack) rotamer_information_from_PDB_stream() (in module pyrosetta.rosetta.core.pack.rotamers) rotamer_library() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) rotamer_library_specification() (pyrosetta.rosetta.core.chemical.ResidueType method) rotamer_library_specification_nonconst() (pyrosetta.rosetta.core.chemical.ResidueType method) rotamer_links() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) rotamer_links_exist() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) rotamer_operations() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) rotamer_recovery() (in module pyrosetta.rosetta.core.pack) rotamer_ref() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) rotamer_sampling_data_xml_schema_attributes() (in module pyrosetta.rosetta.core.pack.task.operation) rotamer_set_contains_rotamer() (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) rotamer_set_operation_begin() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) rotamer_set_operation_end() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) rotamer_sets() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover method) rotamer_trials() (in module pyrosetta.rosetta.core.pack) RotamerBoltzmannWeight2 (class in pyrosetta.rosetta.protocols.simple_filters) RotamerBoltzmannWeightEvaluator (class in pyrosetta.rosetta.protocols.toolbox) RotamerBoltzmannWeightFeaturesCreator (class in pyrosetta.rosetta.protocols.features) RotamerBuildingData (class in pyrosetta.rosetta.core.pack.dunbrack) RotamerConstraint (class in pyrosetta.rosetta.core.pack.dunbrack) RotamerDots (class in pyrosetta.rosetta.core.pack.interaction_graph) RotamerDotsCache (class in pyrosetta.rosetta.core.pack.interaction_graph) RotamerDotsRadiusData (class in pyrosetta.rosetta.core.pack.interaction_graph) RotamerDumpMover (class in pyrosetta.rosetta.protocols.RotamerDump) RotamerExplosion (class in pyrosetta.rosetta.core.pack.task.operation) RotamerFeaturesCreator (class in pyrosetta.rosetta.protocols.features) RotamerizeMover (class in pyrosetta.rosetta.protocols.simple_moves) RotamerLibrary (class in pyrosetta.rosetta.core.pack.dunbrack) RotamerOperation (class in pyrosetta.rosetta.core.pack.rotamer_set) RotamerRecoveryFactory (class in pyrosetta.rosetta.protocols.rotamer_recovery) RotamerRecoveryFeaturesCreator (class in pyrosetta.rosetta.protocols.features) rotamers_for_trials() (in module pyrosetta.rosetta.protocols.ligand_docking) RotamerSet_ (class in pyrosetta.rosetta.core.pack.rotamer_set) RotamerSubset (class in pyrosetta.rosetta.core.pack.rotamer_set) RotamerTrialsRefiner (class in pyrosetta.rosetta.protocols.loop_modeling.refiners) rotate() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) rotate_anchor_to_x_axis() (in module pyrosetta.rosetta.core.pose.symmetry) rotate_around_atom() (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) rotate_around_downstream_centroid() (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) rotate_into_nucleobase_frame() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) rotate_into_phosphate_frame() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) rotate_pose() (in module pyrosetta.toolbox.numpy_utils) rotate_segment() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) RotateJumpAxisMover (class in pyrosetta.rosetta.protocols.rigid) RotateSegmentMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) rotation() (pyrosetta.rosetta.core.kinematics.Stub method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) rotation_axis() (in module pyrosetta.rosetta.numeric) rotation_by_axis() (pyrosetta.rosetta.core.kinematics.Jump method) rotation_by_matrix() (pyrosetta.rosetta.core.kinematics.Jump method) rotation_matrix() (in module pyrosetta.rosetta.numeric) RotationMover (class in pyrosetta.rosetta.protocols.membrane) RotationMoverCreator (class in pyrosetta.rosetta.protocols.membrane) RotMatrix (class in pyrosetta.rosetta.protocols.mean_field) RotProb (class in pyrosetta.rosetta.protocols.mean_field) round() (in module pyrosetta.rosetta.utility) round_to_float() (in module pyrosetta.rosetta.protocols.features.strand_assembly) round_to_Real() (in module pyrosetta.rosetta.protocols.features.strand_assembly) round_to_Size() (in module pyrosetta.rosetta.protocols.features.strand_assembly) rpad() (in module pyrosetta.rosetta.ObjexxFCL) rpadded() (in module pyrosetta.rosetta.ObjexxFCL) rpm_type1() (in module pyrosetta.rosetta.core.scoring.motif) rpm_type2() (in module pyrosetta.rosetta.core.scoring.motif) rrange() (in module pyrosetta) RRComparer (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRComparerCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRProtocol (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRProtocolCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRReporter (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRReporterCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRReporterHuman (class in pyrosetta.rosetta.protocols.rotamer_recovery) rsd() (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.scoring.AtomNeighbor method) rsd1() (pyrosetta.rosetta.core.id.JumpID method) rsd2() (pyrosetta.rosetta.core.id.JumpID method) rsd_closest_to_chain_com() (in module pyrosetta.rosetta.protocols.membrane) rsd_closest_to_chain_tm_com() (in module pyrosetta.rosetta.protocols.membrane) rsd_closest_to_pose_tm_com() (in module pyrosetta.rosetta.protocols.membrane) rsd_rsd_energy() (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential method) rsd_set_from_cmd_line() (in module pyrosetta.rosetta.core.chemical) rsigma_dot_initializer() (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential method) rstrip() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) rstrip_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) rstripped() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) rstripped_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) rswitch() (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) rt() (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) rt_min() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) run() (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.CartesianMinimizer method) (pyrosetta.rosetta.core.optimization.Minimizer method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) run_boinc_debug() (in module pyrosetta.rosetta.protocols.abinitio)