Index – G

G (pyrosetta.rosetta.protocols.comparative_modeling.features.TorsionBin attribute) G() (in module pyrosetta.rosetta.ObjexxFCL.format) g_radius() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) g_radius_gradient_dx() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) g_radius_gradient_dy() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) g_radius_gradient_dz() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) Ga (pyrosetta.rosetta.core.chemical.element.Elements attribute) GA_Minimizer (class in pyrosetta.rosetta.core.optimization) GA_MINOR (pyrosetta.rosetta.core.scoring.rna.RNA_MotifType attribute) ga_mutation_probability() (pyrosetta.rosetta.core.optimization.MinimizerOptions method) GADockStageParams (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) GALigandDock (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) GALigandDockCreator (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) GAMMA (pyrosetta.rosetta.core.chemical.rna.RNA_Torsion attribute) gamma (pyrosetta.rosetta.core.scoring.APBSConfig.R_PARAM property) (pyrosetta.rosetta.protocols.protein_interface_design.Transformation property) gamma() (pyrosetta.rosetta.core.io.CrystInfo method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.dna.DNABase method) Gamma() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) gamma() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.EulerAngles method) GAMMA_AA (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) gamma_aform() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) GAMMA_ATOM (pyrosetta.rosetta.core.chemical.GreekDistance attribute) GAMMA_CARBOXY_GLUTAMIC_ACID (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes attribute) gamma_components() (pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential method) gamma_cutoff1 (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName property) gamma_cutoff2 (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName property) gammammax (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName property) gammammin (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName property) gammapmax (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName property) gammapmin (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName property) gammatmax (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName property) gammatmin (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName property) GAOptimizer (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) gap_char() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.Sequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) gap_extend() (pyrosetta.rosetta.core.sequence.ChemicalShiftScoringScheme method) (pyrosetta.rosetta.core.sequence.CompassScoringScheme method) (pyrosetta.rosetta.core.sequence.CompositeScoringScheme method) (pyrosetta.rosetta.core.sequence.DPScoringScheme method) (pyrosetta.rosetta.core.sequence.L1ScoringScheme method) (pyrosetta.rosetta.core.sequence.MatrixScoringScheme method) (pyrosetta.rosetta.core.sequence.PairScoringScheme method) (pyrosetta.rosetta.core.sequence.ProfSimScoringScheme method) (pyrosetta.rosetta.core.sequence.ScoringScheme method) (pyrosetta.rosetta.core.sequence.SimpleScoringScheme method) gap_open() (pyrosetta.rosetta.core.sequence.ChemicalShiftScoringScheme method) (pyrosetta.rosetta.core.sequence.CompassScoringScheme method) (pyrosetta.rosetta.core.sequence.CompositeScoringScheme method) (pyrosetta.rosetta.core.sequence.DPScoringScheme method) (pyrosetta.rosetta.core.sequence.L1ScoringScheme method) (pyrosetta.rosetta.core.sequence.MatrixScoringScheme method) (pyrosetta.rosetta.core.sequence.PairScoringScheme method) (pyrosetta.rosetta.core.sequence.ProfSimScoringScheme method) (pyrosetta.rosetta.core.sequence.ScoringScheme method) (pyrosetta.rosetta.core.sequence.SimpleScoringScheme method) gap_size() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) gap_size_to_anchor() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) gap_solved() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) GapCloser (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover) gapped_positions() (pyrosetta.rosetta.core.sequence.SequenceAlignment method) GapSolutionPicker (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers) garbage_collection() (pyrosetta.rosetta.protocols.jd2.DebugOut_MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd2.MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd2.WriteOut_MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd3.JobGenealogist method) gasteiger_atom_type() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.ResidueType method) gasteiger_atom_type_set() (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) gasteiger_atom_typeset() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) GasteigerAtomTypeData (class in pyrosetta.rosetta.core.chemical.gasteiger) GasteigerAtomTypeData.AtomicOrbitalTypes (class in pyrosetta.rosetta.core.chemical.gasteiger) GasteigerAtomTypeData.HybridOrbitalType (class in pyrosetta.rosetta.core.chemical.gasteiger) GasteigerAtomTypeData.PiContributionType (class in pyrosetta.rosetta.core.chemical.gasteiger) GasteigerAtomTypeData.Properties (class in pyrosetta.rosetta.core.chemical.gasteiger) GasteigerAtomTypeData.TypeDifference (class in pyrosetta.rosetta.core.chemical.gasteiger) GasteigerAtomTypeSet (class in pyrosetta.rosetta.core.chemical.gasteiger) gate_pssm_scores() (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) gate_svm_scores() (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) gather_coords() (in module pyrosetta.rosetta.protocols.comparative_modeling) GatherPosesMover (class in pyrosetta.rosetta.protocols.cluster) GAUCHE_EFFECT (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType attribute) gauss (pyrosetta.rosetta.core.scoring.ScoreType attribute) gauss() (in module pyrosetta.rosetta.core.scoring.epr_deer) Gaussian (pyrosetta.rosetta.protocols.ligand_docking.Distribution attribute) gaussian() (in module pyrosetta.rosetta.numeric.random) (pyrosetta.rosetta.core.scoring.SmoothScoreTermCoeffs method) (pyrosetta.rosetta.numeric.random.RandomGenerator method) gaussian_deriv() (in module pyrosetta.rosetta.core.scoring.constraints) gaussian_jump_move() (in module pyrosetta.rosetta.protocols.rigid) gaussian_move() (pyrosetta.rosetta.core.kinematics.Jump method) gaussian_move_single_rb() (pyrosetta.rosetta.core.kinematics.Jump method) gaussian_parameter_set_alpha() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_beta() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_chi_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_chi_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_delta_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_delta_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_epsilon_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_epsilon_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_gamma() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_nu1_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_nu1_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_nu2_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_nu2_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_zeta_alpha_ap() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_zeta_alpha_sc_minus() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_parameter_set_zeta_alpha_sc_plus() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) gaussian_random_xform() (in module pyrosetta.rosetta.numeric.random) gaussian_stdev() (in module pyrosetta.rosetta.protocols.recces) GaussianChainDoubleFunc (class in pyrosetta.rosetta.core.scoring.func) GaussianChainFunc (class in pyrosetta.rosetta.core.scoring.func) GaussianChainFuncPotentialEvaluator (class in pyrosetta.rosetta.core.scoring.loop_graph.evaluator) GaussianChainGeneralFunc (class in pyrosetta.rosetta.core.scoring.func) GaussianChainQuadrupleFunc (class in pyrosetta.rosetta.core.scoring.func) GaussianChainSingleFunc (class in pyrosetta.rosetta.core.scoring.func) GaussianChainTripleFunc (class in pyrosetta.rosetta.core.scoring.func) GaussianFunc (class in pyrosetta.rosetta.core.scoring.func) GaussianOverlapEnergy (class in pyrosetta.rosetta.core.energy_methods) GaussianOverlapEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) GaussianParameter (class in pyrosetta.rosetta.core.chemical.rna) GaussianRBSegmentMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) gb_elec (pyrosetta.rosetta.core.scoring.ScoreType attribute) GB_GET_ALL_BORN_RADII (pyrosetta.rosetta.basic.ProfTag attribute) GB_SETUP_FOR_PACKING (pyrosetta.rosetta.basic.ProfTag attribute) gc() (pyrosetta.rosetta.cppdb.pool method) gcount() (pyrosetta.rosetta.utility.io.izstream method) Gd (pyrosetta.rosetta.core.chemical.element.Elements attribute) GDB (class in pyrosetta.rosetta.protocols.sparta) GDBfileName (pyrosetta.rosetta.protocols.sparta.GDB property) GDT() (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilter method) gdt_by_TM() (pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator method) GDTHA (pyrosetta.rosetta.core.scoring.TMscoreStore property) gdtha() (in module pyrosetta.rosetta.core.scoring) GDThatonative() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) gdtsc() (in module pyrosetta.rosetta.core.scoring) GDTTS (pyrosetta.rosetta.core.scoring.TMscoreStore property) Ge (pyrosetta.rosetta.core.chemical.element.Elements attribute) ge() (pyrosetta.rosetta.utility.vectorL_ZeroSelector_false_t static method) (pyrosetta.rosetta.utility.vectorL_ZeroSelector_true_t static method) gen_bonded (pyrosetta.rosetta.core.scoring.ScoreType attribute) gen_bonded_angle (pyrosetta.rosetta.core.scoring.ScoreType attribute) gen_bonded_bond (pyrosetta.rosetta.core.scoring.ScoreType attribute) GEN_BONDED_EXCL_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) gen_bonded_improper (pyrosetta.rosetta.core.scoring.ScoreType attribute) gen_bonded_lr (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) gen_bonded_torsion (pyrosetta.rosetta.core.scoring.ScoreType attribute) gen_born_lr (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) GEN_BORN_POSE_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) GEN_BORN_ROTAMER_BACKGROUND_ENERGIES (pyrosetta.rosetta.basic.ProfTag attribute) GEN_BORN_ROTAMER_PAIR_ENERGIES (pyrosetta.rosetta.basic.ProfTag attribute) GEN_BORN_ROTAMER_SET_INFO (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum attribute) gen_diversity_pool() (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) gen_dynamic_patches() (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) gen_evaluation_output() (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) gen_intf_contact_map() (in module pyrosetta.rosetta.protocols.glycan_docking) genbonded_score_full() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) genbonded_score_hybrid() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) GenBondedExclInfo (class in pyrosetta.rosetta.core.scoring) GenBornEnergy (class in pyrosetta.rosetta.core.energy_methods) GenBornEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) GenBornPoseInfo (class in pyrosetta.rosetta.core.scoring) GenBornPotential (class in pyrosetta.rosetta.core.scoring) GenBornResidueInfo (class in pyrosetta.rosetta.core.scoring) GenBornRotamerSetInfo (class in pyrosetta.rosetta.core.scoring) geneate_pose_from_old_state (pyrosetta.rosetta.protocols.pack_daemon.DaemonSetMessage attribute) general (pyrosetta.rosetta.protocols.network.UIObserver.ObserverType attribute) general() (in module pyrosetta.rosetta.ObjexxFCL.format) general_base_pair_step_library() (pyrosetta.rosetta.core.import_pose.libraries.RNA_LibraryManager method) general_name (pyrosetta.rosetta.core.chemical.rings.RingConformer property) general_observer (pyrosetta.rosetta.protocols.moves.PyMOLObserver attribute) (pyrosetta.rosetta.protocols.moves.PyMOLObserver.ObserverType attribute) general_set_phi() (in module pyrosetta.rosetta.protocols.generalized_kinematic_closure) general_set_psi() (in module pyrosetta.rosetta.protocols.generalized_kinematic_closure) GeneralAntibodyModeler (class in pyrosetta.rosetta.protocols.antibody.design) GeneralEvent (class in pyrosetta.rosetta.core.conformation.signals) (class in pyrosetta.rosetta.core.pose.signals) generalEvent() (pyrosetta.rosetta.protocols.moves.PyMOLObserver method) (pyrosetta.rosetta.protocols.network.UIObserver method) GeneralFileContents (class in pyrosetta.rosetta.utility.io) GeneralFileContentsVector (class in pyrosetta.rosetta.utility.io) GeneralFileManager (class in pyrosetta.rosetta.utility.io) GeneralFileManagerVector (class in pyrosetta.rosetta.utility.io) generalized_monte_carlo (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocolEnum attribute) GeneralizedKIC (class in pyrosetta.rosetta.protocols.generalized_kinematic_closure) GeneralizedKICCreator (class in pyrosetta.rosetta.protocols.generalized_kinematic_closure) GeneralizedKICfilter (class in pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter) GeneralizedKICperturber (class in pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber) GeneralizedKICselector (class in pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector) generate_alc_ensemble_for_region() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) generate_assembly() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) generate_atom_positions() (in module pyrosetta.rosetta.protocols.helical_bundle) generate_backrub_ensemble_for_region() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) generate_batch() (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) generate_bb_coordinate_constraints() (in module pyrosetta.rosetta.protocols.relax) generate_beta_database_test() (in module pyrosetta.rosetta.protocols.stepwise.sampler.protein) generate_binary_score_file() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) generate_centroid_constraints() (in module pyrosetta.rosetta.protocols.hybridization) generate_claims() (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) generate_combinations_of_motif_fragments_by_delta_variation() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) generate_constraint_files() (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) generate_constraints() (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleResidueInvrotTarget method) generate_counts() (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) generate_csts() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMover method) generate_data() (pyrosetta.rosetta.core.scoring.epr_deer.DEERIO method) generate_data_for_input_pose_id() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.TagManager method) generate_edge_file() (pyrosetta.rosetta.protocols.sewing.hashing.EdgeMapGenerator method) generate_edges() (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) generate_empty_jump_frame() (in module pyrosetta.rosetta.protocols.jumping) generate_ensemble_for_region() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) generate_explicit_ligand_rotamer_poses() (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) generate_fa_and_cen_constraints() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList method) generate_frame() (pyrosetta.rosetta.protocols.jumping.ResiduePairJump method) generate_from_frag_file() (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist method) generate_from_fragments() (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist method) generate_from_sequence() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) generate_full_tracer_report() (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) generate_fullatom_constraints() (in module pyrosetta.rosetta.protocols.hybridization) generate_human_readable_documentation() (in module pyrosetta.rosetta.utility.xsd_util) generate_human_readable_recursive() (in module pyrosetta.rosetta.utility.xsd_util) generate_human_readable_summary() (in module pyrosetta.rosetta.utility.xsd_util) generate_insert_map() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragSetCollection method) (pyrosetta.rosetta.core.fragment.MinimalFragSet method) (pyrosetta.rosetta.core.fragment.OrderedFragSet method) generate_inverse_rotamer_constraints() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) generate_jump_frags() (pyrosetta.rosetta.protocols.abinitio.FixTemplateJumpSetup method) (pyrosetta.rosetta.protocols.abinitio.TemplateJumpSetup method) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.BasePairingLibrary method) (pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.JumpSample method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.PairingLibrary method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) (pyrosetta.rosetta.protocols.jumping.SpecificGeometryLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) generate_jump_frame() (in module pyrosetta.rosetta.protocols.jumping) generate_jump_frames() (pyrosetta.rosetta.protocols.jumping.JumpSample method) generate_key() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) (pyrosetta.rosetta.protocols.sewing.hashing.Hasher method) generate_ligand_key() (pyrosetta.rosetta.protocols.sewing.hashing.LigandBindingResPlacer static method) generate_lookback_rmsd() (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) generate_match_pose() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) generate_metapatched_variants() (pyrosetta.rosetta.protocols.residue_optimization.MetapatchEnumeration method) generate_monte_carlo_move() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_FinalFullatomRefinementMoveGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_HelixCoilMoveGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator method) generate_mover() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) generate_mover_for_protocol() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) generate_mover_xml_string() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) generate_N2C_cyclic_peptide_protein_complex() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) generate_native_rotamers_map() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) generate_nonstandard_residue_set() (in module pyrosetta) generate_output_pose() (pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop method) generate_overlaps() (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) generate_perturbed_value() (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) generate_pose_from_packer_description() (in module pyrosetta.rosetta.core.pack.interaction_graph) generate_pose_specific_data() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) generate_prob() (in module pyrosetta.rosetta.core.io.external) generate_profile_from_seq() (pyrosetta.rosetta.protocols.splice.SpliceManager method) generate_profile_score() (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) generate_profile_score_wo_background() (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) generate_relax_from_cmd() (in module pyrosetta.rosetta.protocols.relax) generate_remodel_constraints() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) generate_replacement_restype() (in module pyrosetta.rosetta.core.util) generate_resfile_from_pdb() (in module pyrosetta.toolbox.generate_resfile) generate_resfile_from_pose() (in module pyrosetta.toolbox.generate_resfile) generate_residue_subset_fragment_store() (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore method) generate_restype() (pyrosetta.rosetta.core.chemical.rdkit.RDMolToRestype method) generate_reversed() (pyrosetta.rosetta.core.scoring.dssp.Pairing method) generate_roc_curve() (pyrosetta.rosetta.numeric.RocCurve method) generate_scaffold_matches() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) generate_search_points() (pyrosetta.rosetta.protocols.hotspot_hashing.CartesianSearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.RotationSearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.SphericalRotationSearchPattern method) generate_secstruct_for_length() (in module pyrosetta.rosetta.protocols.denovo_design.architects) generate_seqmap_from_poses() (in module pyrosetta.rosetta.protocols.constraint_generator) generate_sequence_claims() (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) generate_sequence_profile() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) generate_start_pose() (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) generate_stub_rmsd() (pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop method) generate_sub_fragment() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.FragData method) generate_sub_frame() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) generate_tag() (pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet method) generate_tag_given_options() (in module pyrosetta.rosetta.utility.xsd_util) generate_targets_and_inverse_rotamers() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) generate_task_op_all_cdr_design() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) generate_task_op_cdr_design() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) generate_task_op_cdr_profiles() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) generate_taskfactory_and_add_task_awareness() (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) generate_tf_seq_design() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) generate_tf_seq_design_graft_design() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) generate_unique_name() (in module pyrosetta.rosetta.protocols.ligand_docking) generate_unique_structure_id() (in module pyrosetta.rosetta.protocols.wum) generateIcosahedralSamples() (pyrosetta.rosetta.numeric.UniformRotationSampler method) GenerateMainchainPotential (class in pyrosetta.rosetta.protocols.mainchain_potential) GenerateMainchainPotentialOptions (class in pyrosetta.rosetta.protocols.mainchain_potential) GenerateMap() (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot method) generates_aa() (pyrosetta.rosetta.core.chemical.Patch method) generates_base_residue_type() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AddProtonChi method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeAncestory method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.RenameAtom method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.Set_AA method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetBaseName method) (pyrosetta.rosetta.core.chemical.SetDisulfideAtomName method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) generates_interchangeability_group() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AddProtonChi method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeAncestory method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.RenameAtom method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.Set_AA method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetBaseName method) (pyrosetta.rosetta.core.chemical.SetDisulfideAtomName method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) generates_name3() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AddProtonChi method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeAncestory method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.RenameAtom method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.Set_AA method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetBaseName method) (pyrosetta.rosetta.core.chemical.SetDisulfideAtomName method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) generates_new_name3() (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) generates_patched_residue_type_with_interchangeability_group() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) generates_patched_residue_type_with_name3() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) generates_primary_hits() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) GenerateStoredRBConfs (class in pyrosetta.rosetta.protocols.enzdes) generation_tag() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) generations() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) generations_checkpoint_filename() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) generators() (pyrosetta.rosetta.core.scoring.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) generic() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties method) GenericBondedEnergy (class in pyrosetta.rosetta.core.energy_methods) GenericBondedEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) GenericBondedPotential (class in pyrosetta.rosetta.core.scoring) GenericJobInputter (class in pyrosetta.rosetta.protocols.comparative_modeling) GenericJobInputterCreator (class in pyrosetta.rosetta.protocols.comparative_modeling) GenericMonteCarloMover (class in pyrosetta.rosetta.protocols.monte_carlo) GenericMonteCarloMoverCreator (class in pyrosetta.rosetta.protocols.monte_carlo) GenericRemodelConstraintGenerator (class in pyrosetta.rosetta.protocols.forge.remodel) GenericResidueConnectionData (class in pyrosetta.rosetta.core.scoring.etable.etrie) GenericSimulatedAnnealer (class in pyrosetta.rosetta.protocols.monte_carlo) GenericSimulatedAnnealerCreator (class in pyrosetta.rosetta.protocols.monte_carlo) GeneticAlgorithm (class in pyrosetta.rosetta.protocols.genetic_algorithm) GeneticAlgorithmBase (class in pyrosetta.rosetta.protocols.genetic_algorithm) GenKICPerturberEffect (class in pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber) GenMeanFieldMover (class in pyrosetta.rosetta.protocols.mean_field) GenMeanFieldMoverCreator (class in pyrosetta.rosetta.protocols.mean_field) GenPharmacophore (class in pyrosetta.rosetta.protocols.pockets) GenTorsionParams (class in pyrosetta.rosetta.core.scoring) genWigner_ds() (pyrosetta.rosetta.numeric.fourier.SO3coeffs method) geo_dim_type_from_name() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) geom_cst_id() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) geom_csts_downstream_output() (pyrosetta.rosetta.protocols.match.MatcherTask method) geom_id() (pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage method) geom_sol (pyrosetta.rosetta.core.scoring.ScoreType attribute) geom_sol_fast (pyrosetta.rosetta.core.scoring.ScoreType attribute) geom_sol_fast_intra_RNA (pyrosetta.rosetta.core.scoring.ScoreType attribute) geom_sol_interres_path_distance_cutoff() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) geom_sol_intra_RNA (pyrosetta.rosetta.core.scoring.ScoreType attribute) geom_sol_intrares_path_distance_cutoff() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) GEOM_SOLV_NBLIST (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) geom_solv_pair_nblist (pyrosetta.rosetta.core.scoring.min_pair_data attribute) geometric_dimension() (pyrosetta.rosetta.core.scoring.hbonds.Polynomial_1d method) geometric_sol_one_way_bb_bb() (pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator method) geometric_sol_one_way_sc() (pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator method) GeometricFunc (class in pyrosetta.rosetta.protocols.moves) GeometricSolEnergyEvaluator (class in pyrosetta.rosetta.core.scoring.geometric_solvation) GeometricSolvationFeatures (class in pyrosetta.rosetta.protocols.features) GeometricSolvationFeaturesCreator (class in pyrosetta.rosetta.protocols.features) geometry (pyrosetta.rosetta.protocols.buns.CALCULATORMODE attribute) geometry() (pyrosetta.rosetta.protocols.hybridization.FragmentBiasAssigner method) geometry_enum() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) geometry_is_initialized() (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet method) geometry_score_threshold (pyrosetta.rosetta.protocols.sewing.data_storage.LigandDescription property) geometry_string() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) GeometryFilter (class in pyrosetta.rosetta.protocols.score_filters) GeometryFilterCreator (class in pyrosetta.rosetta.protocols.score_filters) GeometrySecMatchRPE (class in pyrosetta.rosetta.protocols.match.downstream) GeomSampleInfo (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) get() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.bindings.pose.PoseResidueLabelMaskAccessor method) (pyrosetta.bindings.pose.PoseScoreAccessor method) (pyrosetta.io.silent_file_map.SilentFileEnergyAccessor method) (pyrosetta.io.silent_file_map.SilentFileMap method) (pyrosetta.io.silent_file_map.SilentFilePoseAccessor method) (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.DataCache_basic_datacache_CacheableData_t method) (pyrosetta.rosetta.basic.datacache.DataCache_CacheableData method) (pyrosetta.rosetta.basic.datacache.DataCache_core_pose_datacache_CacheableObserver_t method) (pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationFactory method) (pyrosetta.rosetta.core.id.AtomID_Map_AtomID method) (pyrosetta.rosetta.core.id.AtomID_Map_bool method) (pyrosetta.rosetta.core.id.AtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_MP_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_Real method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_NamedAtomID method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryFactory method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.metrics.EnergyDependentCalculator method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricCalculator method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.InterfaceDefinitionCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.InterfaceDeltaEnergeticsCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.InterfaceNeighborDefinitionCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.InterfaceSasaDefinitionCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.SasaCalculator2 method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.SasaCalculatorLegacy method) (pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator method) (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet method) (pyrosetta.rosetta.core.scoring.saxs.DistanceHistogram method) (pyrosetta.rosetta.core.scoring.saxs.FormFactor method) (pyrosetta.rosetta.cppdb.connection_info method) (pyrosetta.rosetta.cppdb.ref_ptr_cppdb_backend_connection_t method) (pyrosetta.rosetta.cppdb.ref_ptr_cppdb_backend_loadable_driver_t method) (pyrosetta.rosetta.cppdb.ref_ptr_cppdb_backend_statement_t method) (pyrosetta.rosetta.cppdb.ref_ptr_cppdb_pool_t method) (pyrosetta.rosetta.numeric.AxisRotationSampler method) (pyrosetta.rosetta.numeric.UniformRotationSampler method) (pyrosetta.rosetta.protocols.buns.BuriedUnsatisfiedPolarsCalculator2 method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HPool_RMSD method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.Pool_RMSD method) (pyrosetta.rosetta.protocols.denovo_design.calculators.CavityCalculator method) (pyrosetta.rosetta.protocols.fldsgn.NcontactsCalculator method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) (pyrosetta.rosetta.protocols.mean_field.EnergiesByTaskCalculator method) (pyrosetta.rosetta.protocols.neighbor.Neighborhood method) (pyrosetta.rosetta.protocols.pose_metric_calculators.CatPiCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.ChargeCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.ClashCountCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.FragQualCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.HPatchCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.MetricValueGetter method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborsByDistanceCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NonlocalContactsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.PackstatCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.PiPiCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.ResidueDecompositionByChainCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.ResidueDecompositionCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.RotamerBoltzCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SaltBridgeCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SemiExplicitWaterUnsatisfiedPolarsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SHOBuriedUnsatisfiedPolarsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SurfaceCalculator method) (pyrosetta.rosetta.protocols.simple_pose_metric_calculators.BuriedUnsatisfiedPolarsCalculator method) (pyrosetta.rosetta.protocols.simple_pose_metric_calculators.NumberHBondsCalculator method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDistSasaCalculator method) (pyrosetta.rosetta.std.ifstream method) (pyrosetta.rosetta.std.iostream method) (pyrosetta.rosetta.std.istream method) (pyrosetta.rosetta.std.istringstream method) (pyrosetta.rosetta.std.stringstream method) (pyrosetta.rosetta.std.wistream method) (pyrosetta.rosetta.utility.DenseBoolMap_5_0_t method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_core_kinematics_MoveMap_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_core_pose_Pose_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_core_scoring_bin_transitions_BinTransitionCalculator_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_protocols_antibody_AntibodyInfo_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_protocols_loops_Loops_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_chemical_AtomProperties_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_chemical_ResidueProperties_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_chemical_rotamers_RotamerLibrarySpecification_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_kinematics_MoveMap_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_pose_Pose_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_scoring_ScoreFunction_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_interpolation_spline_BicubicSpline_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_interpolation_spline_CubicSpline_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_interpolation_spline_PolycubicSplineBase_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_MathNTensorBase_double_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_protocols_loops_Loops_t method) (pyrosetta.rosetta.utility.thread.MutableCache_const_core_chemical_ResidueTypeSet__star__core_pack_palette_BaseTypeList_t method) get_10A_neighbors() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) get_1b_energy() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) get_2b_energy() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) get_2D_histogram() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics method) get_2d_torsion() (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler2D method) get_2way_orientation() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) get_3_letter_codes_from_NA_consensus_sequence() (in module pyrosetta.rosetta.core.enzymes) get_3_letter_codes_from_peptide_consensus_sequence() (in module pyrosetta.rosetta.core.enzymes) get_3d_torsion() (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler3D method) get_5_ss_models_from_db() (in module pyrosetta.rosetta.protocols.legacy_sewing) get_6D_trans_rot_potential_evaluator() (in module pyrosetta.rosetta.core.scoring.loop_graph) get_A() (in module pyrosetta.rosetta.core.scoring.electron_density) (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) get_a() (pyrosetta.rosetta.protocols.pockets.UnionEdge method) get_A() (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) get_A_all() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter method) get_a_axis() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_A_index() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_per_lanthanides method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_per_lanthanides_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_per_lanthanides_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_per_lanthanides_Ts4 method) get_aa() (pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecification method) (pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet method) get_aa_for_state() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_aa_submatrix_energies() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) get_aa_submatrix_energies_for_edge() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) get_aa_type() (pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex method) get_aas_allowed() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) get_ab_cdr_bfactors() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper static method) get_ab_design_dock_high_scorefxn() (in module pyrosetta.rosetta.protocols.antibody.design) get_ab_design_dock_low_scorefxn() (in module pyrosetta.rosetta.protocols.antibody.design) get_ab_design_global_scorefxn() (in module pyrosetta.rosetta.protocols.antibody.design) get_ab_design_min_scorefxn() (in module pyrosetta.rosetta.protocols.antibody.design) get_ab_OCDs() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper static method) get_ab_region_outliers() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper static method) get_abego() (in module pyrosetta.rosetta.core.sequence) get_abego_string() (pyrosetta.rosetta.core.sequence.ABEGOManager method) get_ABGEO_string() (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) get_abort_on_failed_loop() (pyrosetta.rosetta.protocols.LoopRebuild method) get_absolute_threshold() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerElecDensDiff method) get_accept_aborted_loops() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) get_accept_rate() (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) get_accessible_states() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) get_accuracy_weight() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential method) get_add_constraints() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) get_add_or_delete_element() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) get_add_probability() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_additional_output() (pyrosetta.rosetta.core.chemical.modifications.ChemistryBase method) (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop 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.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder 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.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.chemistries.Chemistry method) (pyrosetta.rosetta.protocols.chemistries.PatchChemistry method) (pyrosetta.rosetta.protocols.chemistries.WrappedBaseChemistry method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover 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.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover 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.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize 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.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.forge.components.BDR 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.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) (pyrosetta.rosetta.protocols.hydrate.Hydrate method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover 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.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM 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_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover 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.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover 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.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DsspMover method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.Mover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover 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.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot 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.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop 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.PrepackMover 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.SecretionOptimizationMover 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.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover 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.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover 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.IdealizeHelicesMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax 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.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover 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.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover 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_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover 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.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover 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.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover 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.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.star.StarAbinitio 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.SideChainCopier method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler 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.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover 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.monte_carlo.StepWiseMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) get_additional_output_false_mover() (pyrosetta.rosetta.protocols.moves.IfMover method) get_additional_output_true_mover() (pyrosetta.rosetta.protocols.moves.IfMover method) get_additional_output_with_rmsd() (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) get_additional_task_operarations() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockTaskFactory method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) get_address() (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) get_addresses_at_level() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) get_adjacent_heavy_atoms() (pyrosetta.rosetta.core.conformation.Residue method) get_adjacent_node() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NodeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) get_adjacent_otf_node() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) get_adjacent_symmin_node() (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) get_adjacent_symmlinmem_node() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) get_ads_secondary_struct() (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) get_AHDangle() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) get_akash_dyepos() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_al_tensor_max_z() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) get_al_tensor_trace() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) get_ala_pose() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_align_depth() (pyrosetta.rosetta.core.fragment.rna.FragmentLibrary method) get_aligner() (pyrosetta.rosetta.core.sequence.AlignerFactory static method) get_alignment() (pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator method) (pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator method) (pyrosetta.rosetta.protocols.evaluation.AlignEvaluator method) get_alignment_atoms() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) get_alignment_domain() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) get_alignment_from_template() (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) get_alignment_medium_label() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) get_alignpdbinfotosequencesmode_from_string() (in module pyrosetta.rosetta.protocols.pdbinfo_manipulations) get_all() (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) get_all_alignments() (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentGenerator method) get_all_atom_types_in_database() (pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO method) get_all_born_radii() (pyrosetta.rosetta.core.scoring.GenBornPotential method) get_all_cdrs() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_all_cdrs_present() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_all_channels_string() (pyrosetta.rosetta.basic.MemTracer static method) (pyrosetta.rosetta.basic.MemTracerImpl static method) (pyrosetta.rosetta.basic.Tracer static method) (pyrosetta.rosetta.basic.TracerImpl static method) get_all_comments() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) get_all_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) get_all_data() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_all_derivs() (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_1_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_2_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_3_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_4_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_5_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_6_t method) get_all_disulfides() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingDatabase method) get_all_exemplars() (pyrosetta.rosetta.protocols.cluster.APCluster method) get_all_features_names() (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) get_all_function_names() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) get_all_glycans_and_neighbor_res_task_factory() (in module pyrosetta.rosetta.protocols.carbohydrates) get_all_graft_permutations() (in module pyrosetta.rosetta.protocols.antibody.design) get_all_jacobians() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) get_all_loops_closed() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) get_all_loops_definer_names() (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) get_all_nondegenerate_conformers() (pyrosetta.rosetta.core.chemical.rings.RingConformerSet method) get_all_per_residue_data() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_all_poseOPs() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector method) get_all_poses() (pyrosetta.rosetta.core.import_pose.pose_stream.ExtendedPoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.LazySilentFilePoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.MetaPoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.PDBPoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.PoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.SilentFilePoseInputStream method) get_all_possible_residue_types() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) get_all_properties() (pyrosetta.rosetta.core.chemical.AtomType method) get_all_register_and_bulges() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) get_all_res_list() (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo) get_all_residues() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_all_residues_in_database() (pyrosetta.rosetta.core.chemical.ResidueDatabaseIO method) get_all_residues_in_this_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_all_rotamer_samples() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) get_all_score_line_strings() (in module pyrosetta.rosetta.core.pose) get_all_scores() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyAssemblyScoreFunction method) get_all_sm_data() (pyrosetta.rosetta.core.simple_metrics.SimpleMetricData method) get_all_solutions() (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) get_all_states() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) get_all_types_with_variants_aa() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_all_types_with_variants_by_basetype() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_all_types_with_variants_name1() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_all_types_with_variants_name3() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_all_working_moving_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_AllCDRs_in_loopsop() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_allocator() (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairSet method) (pyrosetta.rosetta.std.list_const_protocols_match_Hit__star__t method) (pyrosetta.rosetta.std.list_core_id_AtomID_t method) (pyrosetta.rosetta.std.list_core_io_rcsb_ExperimentalTechnique_t method) (pyrosetta.rosetta.std.list_core_scoring_custom_pair_distance_atoms_and_func_struct_t method) (pyrosetta.rosetta.std.list_core_scoring_power_diagram_PDvertex__star__t method) (pyrosetta.rosetta.std.list_double_t method) (pyrosetta.rosetta.std.list_int_t method) (pyrosetta.rosetta.std.list_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.list_protocols_match_Hit_t method) (pyrosetta.rosetta.std.list_protocols_multistage_rosetta_scripts_mover_or_filter_t method) (pyrosetta.rosetta.std.list_protocols_pockets_spherical_coor_triplet_t method) (pyrosetta.rosetta.std.list_RDKit_Atom__star__t method) (pyrosetta.rosetta.std.list_RDKit_Bond__star__t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BasePair_t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BaseStack_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_double_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.list_std_set_std_string_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_operation_ResLvlTaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_chunk_library_inputters_ChunkLibraryInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_full_model_inputters_FullModelInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_inputters_PoseInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_PoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_SecondaryPoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_XMLSchemaParticle_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_interaction_graph_AnnealableGraphBase_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_rotamer_set_RotamerOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_task_operation_TaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_power_diagram_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_deallocation_DeallocationMessage_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_LarvalJob_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_output_OutputSpecification_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_pose_outputters_SecondaryPoseOutputter_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_CrossPeak_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.std.list_std_string_t method) (pyrosetta.rosetta.std.list_unsigned_long_t method) (pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t method) (pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t method) (pyrosetta.rosetta.std.list_utility_tag_XMLSchemaSimpleSubelementList_ElementSummary_t method) (pyrosetta.rosetta.std.list_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.list_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.std.multimap_double_std_pair_unsigned_long_std_pair_std_shared_ptr_protocols_hotspot_hashing_HotspotStubSet_std_shared_ptr_protocols_hotspot_hashing_HotspotStub_t method) (pyrosetta.rosetta.std.multimap_double_std_shared_ptr_protocols_hotspot_hashing_HotspotStub_t method) (pyrosetta.rosetta.std.set_core_chemical_gasteiger_GasteigerAtomTypeData_AtomicOrbitalTypes_t method) (pyrosetta.rosetta.std.set_core_id_DOF_ID_t method) (pyrosetta.rosetta.std.set_core_id_PartialAtomID_t method) (pyrosetta.rosetta.std.set_double_t method) (pyrosetta.rosetta.std.set_int_t method) (pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t method) (pyrosetta.rosetta.std.set_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.set_std_set_unsigned_long_t method) (pyrosetta.rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_t method) (pyrosetta.rosetta.std.set_std_string_t method) (pyrosetta.rosetta.std.set_unsigned_long_t method) (pyrosetta.rosetta.std.unordered_map_basic_datacache_ResRotPair_float_basic_datacache_ResRotPairHasher_std_equal_to_basic_datacache_ResRotPair_std_allocator_std_pair_const_basic_datacache_ResRotPair_float_t method) (pyrosetta.rosetta.std.unordered_map_std_pair_char_char_int_core_sequence_CharPairHash_std_equal_to_std_pair_char_char_std_allocator_std_pair_const_std_pair_char_char_int_t method) (pyrosetta.rosetta.std.unordered_map_unsigned_long_numeric_MathMatrix_float_t method) get_allow_anchor_repack() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_allow_glycan_torsion_moves() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) get_allow_independent_alignment_per_fragment_mode() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch method) get_allow_slide_jump_map() (pyrosetta.rosetta.protocols.symmetry.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SymmetrySlider method) get_allowed_failure_before_extend() (pyrosetta.rosetta.protocols.LoopRebuild method) get_allowed_failure_before_stop() (pyrosetta.rosetta.protocols.LoopRebuild method) get_allowed_norm_lin() (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) get_allowed_norm_rot() (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) get_aln() (pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster method) get_alpha() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential method) get_alpha_beta_models_from_db() (in module pyrosetta.rosetta.protocols.legacy_sewing) get_alpha_beta_pattern() (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) get_alphabet() (pyrosetta.rosetta.core.scoring.constraints.ResidueCouplingConstraint method) get_alt_score_() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) get_alt_stateE() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) get_alternate() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) get_alternate_for_node() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) get_alternate_ref() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) get_alternate_state_energy() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge static method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge static method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge static method) get_alternate_state_energy_first_node() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge static method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge static method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge static method) get_alternate_state_energy_second_node() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge static method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge static method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge static method) get_alternative_search_paths() (pyrosetta.rosetta.utility.io.izstream static method) get_amide_mm() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) get_amino_acid_type() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSewingResidue method) get_anchor_and_root_atoms() (in module pyrosetta.rosetta.core.conformation) get_anchor_atomno() (in module pyrosetta.rosetta.core.conformation) get_anchor_noise_constraints_mode() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_anchor_points_for_tmcom() (in module pyrosetta.rosetta.protocols.membrane) get_anchor_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) get_anchor_residue() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) get_anchor_rsd() (in module pyrosetta.rosetta.core.import_pose) get_anchor_via_constraints() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_anchors() (pyrosetta.rosetta.protocols.hybridization.HybridizeFoldtreeDynamic method) get_and_cache_pdb() (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) get_angle() (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) get_angle_cutoff() (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) get_angle_diffs() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) get_angle_max() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) get_angle_multiplier() (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorer method) get_angle_range() (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) get_angles() (in module pyrosetta.rosetta.core.membrane) (in module pyrosetta.rosetta.core.scoring) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) get_angular_momentum_quantum_number() (pyrosetta.rosetta.core.chemical.ElectronConfiguration static method) get_ANN_data() (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib method) get_annealable_graph_summary() (in module pyrosetta.rosetta.core.pack.interaction_graph) get_annealer_observer() (pyrosetta.rosetta.core.pack.annealer.DebuggingAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FASTERAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbCoupledRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbLinkingRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbPwatSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.MultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.annealer.RotamerAssigningAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SequenceSymmetricAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SimAnnealerBase method) (pyrosetta.rosetta.core.pack.annealer.SmartFixbbSimAnnealer method) (pyrosetta.rosetta.protocols.flexpack.annealer.FlexbbSimAnnealer method) get_antibody_chain_ids() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_antibody_chain_string() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_antibody_chains() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_antibody_enum_manager() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_antibody_numbering() (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser method) get_antibody_numbering_info() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_antibody_sequence() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_AntibodyFrameworkInfo() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_antigen_chain_ids() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_antigen_chain_string() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_antigen_chains() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_antiparallel_weight() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) get_apply_offset() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup method) get_arbitrary_score_data_from_pose() (pyrosetta.rosetta.core.io.raw_data.ScoreMap static method) get_arbitrary_string_data_from_pose() (pyrosetta.rosetta.core.io.raw_data.ScoreMap static method) get_area_from_cycle() (in module pyrosetta.rosetta.core.scoring.power_diagram) get_argv() (pyrosetta.rosetta.utility.options.OptionCollection method) get_aro_residues_in_this_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_array() (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_string_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t method) get_assembly_scorer() (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorerFactory method) get_assembly_scorers() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_asu_rotamer() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) get_asymm_unit_fold_tree() (in module pyrosetta.rosetta.core.conformation.symmetry) get_asymmetric_pose_copy_from_symmetric_pose() (in module pyrosetta.rosetta.core.pose.symmetry) get_asymmetric_seqpos() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) get_atom() (pyrosetta.rosetta.core.io.nmr.AtomSelection method) (pyrosetta.rosetta.core.optimization.CartesianMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.scoring.constraints.AtomToAxisConstraint method) (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSewingResidue method) get_atom_atom_carbon_hbond_energy() (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) get_atom_atom_geometric_solvation_for_acceptor() (pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator method) get_atom_atom_geometric_solvation_for_donor() (pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator method) get_atom_bin() (in module pyrosetta.rosetta.core.pose.rna) get_atom_bin_size() (pyrosetta.rosetta.core.pose.rna.VDW_Grid method) get_atom_collision_radius() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) get_atom_coordinates() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) get_atom_coords_xyz() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) get_atom_counts() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) get_atom_derivatives() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingle method) (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingle method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingle method) get_atom_dist_from_connolly_surface() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) get_atom_h2o_hbond_derivative() (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) get_atom_id_map() (pyrosetta.rosetta.core.import_pose.libraries.ChunkSet method) get_atom_IDs() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) get_atom_index() (pyrosetta.rosetta.core.optimization.CartesianMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) get_atom_interaction_radius() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) get_atom_level_domain_map() (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) get_atom_lk_energy() (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) get_atom_name() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) get_atom_name_to_vd_map() (pyrosetta.rosetta.core.chemical.MutableResidueType method) get_atom_pair_func_list() (pyrosetta.rosetta.core.scoring.custom_pair_distance.PairFuncMap method) get_atom_positions() (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) get_atom_radius() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) get_atom_sasa() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_atom_type_property() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_atom_vector() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSewingResidue method) get_atomic_contacting_sidechains() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) get_atomic_number() (pyrosetta.rosetta.core.chemical.Element method) get_atomID() (pyrosetta.rosetta.protocols.normalmode.NormalMode method) get_atomIndexMap_Rd2Res() (pyrosetta.rosetta.core.chemical.rdkit.RestypeToRDMol method) get_atomistic_energies() (in module pyrosetta.rosetta.core.scoring) get_atomname() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) get_atomnames_size() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) get_atoms() (pyrosetta.rosetta.core.kinematics.MoveMap method) get_atoms_ala() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_ala_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_arg() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_arg_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_asn() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_asn_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_asp() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_asp_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_cys() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_cys_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_exocyclic_to_ring_atom() (pyrosetta.rosetta.core.conformation.Residue method) get_atoms_gln() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_gln_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_glu() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_glu_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_gly() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_gly_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_his() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_his_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_ile() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_ile_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_leu() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_leu_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_lys() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_lys_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_met() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_met_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_phe() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_phe_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_pro() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_pro_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_ser() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_ser_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_thr() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_thr_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_trp() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_trp_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_tyr() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_tyr_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_val() (in module pyrosetta.rosetta.core.pose.motif) get_atoms_val_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_AtomVDW() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_attachment_point_string() (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) get_attachments() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) get_author_list() (pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleInfo method) get_autoinitialize() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) get_automorphic_RMSDs() (in module pyrosetta.rosetta.protocols.ligand_docking) get_avail() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) get_average_cation_pi_ip_to_neutral_ip_ratio() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData static method) get_average_cation_sigma_ip_to_neutral_ip_ratio() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData static method) get_average_ip_change_cation_to_neutral() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_average_ip_change_neutral_to_anion() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_average_neutral_pi_ip_to_anion_ip_ratio() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData static method) get_average_neutral_sigma_ip_to_anion_ip_ratio() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData static method) get_averaging_type() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) get_avg_dis_CA_CA() (in module pyrosetta.rosetta.protocols.features.strand_assembly) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) get_avg_dis_strands() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_ax() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) get_axis() (pyrosetta.rosetta.protocols.membrane.FlipMover method) get_b() (pyrosetta.rosetta.protocols.pockets.UnionEdge method) get_b_axis() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_backbone() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) get_backbone_currently_assigned() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) get_backbone_for_current_state() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) get_backbone_list() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) get_backbone_mover() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_backbone_moves() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) get_backbone_reference_frame() (in module pyrosetta.rosetta.core.pose.motif) get_backbone_reference_frame_atomids() (in module pyrosetta.rosetta.core.pose.motif) get_backbone_reference_frame_atomids_with_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_backbone_segment() (pyrosetta.rosetta.protocols.loophash.BackboneDB method) get_backbone_segments() (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) get_backrubmover() (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover method) get_BAHangle() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) get_base_atom_name() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_base_backbone() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) get_base_base_atom_name() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_base_centroid() (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) get_base_centroid_and_rotation_matrix() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) get_base_coordinate_system() (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) get_base_doublet_orientation_from_LW() (in module pyrosetta.rosetta.core.pose.rna) get_base_pair_atoms() (in module pyrosetta.rosetta.core.chemical.rna) get_base_pair_params() (in module pyrosetta.rosetta.core.scoring.dna) get_base_pair_stub_slow() (in module pyrosetta.rosetta.core.scoring.dna) get_base_pairing_info() (in module pyrosetta.rosetta.core.pose.rna) get_base_pairing_list() (in module pyrosetta.rosetta.core.pose.rna) get_base_step_params() (in module pyrosetta.rosetta.core.scoring.dna) get_base_stub() (in module pyrosetta.rosetta.core.scoring.dna) get_base_type_cop() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) get_base_types_aa() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_base_types_name1() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_base_types_name3() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_basic_protein_sampler() (in module pyrosetta.rosetta.protocols.stepwise.sampler.protein) get_basis_map_generator() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_basis_pair() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) get_basis_pair_for_local_segments() (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) get_basis_pair_for_segment() (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) get_basis_pair_for_segment_pair() (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) get_basis_res_bounds() (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) get_batch_description() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) get_batch_id() (in module pyrosetta.rosetta.protocols.features) (pyrosetta.rosetta.protocols.features.ProteinSilentReport method) get_batch_name() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) get_BAtorsion() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) get_bb() (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_bb_alignment_and_transformation() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) get_bb_alignment_and_transformation_wTipsExtraInfo() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) get_bb_atoms_for_residue() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) get_bb_bbE() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets static method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets static method) get_bb_bins() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) get_bb_distance() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) get_bb_for_state() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) get_bb_id() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_bb_ids() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_bb_interface_builder() (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilder method) get_bb_range() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_bb_torsion() (in module pyrosetta.rosetta.core.pose) get_bbcsts() (in module pyrosetta.rosetta.protocols.protein_interface_design) get_bbs() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_begin2() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) get_below_distance_threshold() (pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop method) get_bend_angle() (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) get_best_energy_stub() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) get_best_geometry_score() (pyrosetta.rosetta.protocols.sewing.hashing.LigandBindingResPlacer method) get_best_grid_point() (pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch method) get_best_match_residue_type_for_atom_names() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) get_best_neighboring_shift_RMSD_and_output_silent_file() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) get_best_z() (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) get_bestpose() (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) get_beta() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) get_beta_pairs() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) get_bias_sampling() (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_big_bin() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) get_bin() (pyrosetta.rosetta.core.pose.rna.VDW_Grid method) get_bin_and_pos() (pyrosetta.rosetta.protocols.match.VoxelSetIterator method) get_bin_max() (pyrosetta.rosetta.core.pose.rna.VDW_Grid method) get_bin_offset() (pyrosetta.rosetta.core.pose.rna.VDW_Grid method) get_bin_size() (pyrosetta.rosetta.core.scoring.func.SplineFunc method) get_bin_transition_calculator() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculatorManager method) get_binary_name() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) get_binary_rna_silent_struct_safe() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) get_binary_rna_silent_struct_safe_wrapper() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) get_binding_cycles() (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_binding_energy() (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_Potential method) get_bins() (in module pyrosetta.rosetta.core.scoring.motif) get_bins_per_A2() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) get_bins_vect() (pyrosetta.rosetta.core.scoring.func.SplineFunc method) get_bins_vect_size() (pyrosetta.rosetta.core.scoring.func.SplineFunc method) get_boltzman_factor() (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel method) get_boltzmann_rotamer_mover() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_boltzmann_temp() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) get_bond_length() (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) get_bonus_map() (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) get_bonus_score() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) get_bool() (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_string_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t method) get_bool_idx() (in module pyrosetta.rosetta.core.scoring.rna.data) get_boolean_option() (in module pyrosetta.rosetta.basic.options) get_boolean_vector_option() (in module pyrosetta.rosetta.basic.options) get_bound_mut_pose() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) get_bound_wt_pose() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) get_boundary_functions() (pyrosetta.rosetta.numeric.interpolation.spline.SplineGenerator method) get_boundary_neighs() (pyrosetta.rosetta.core.energy_methods.FAElecContextData method) get_boundary_residues() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_boundary_selector() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_branches() (pyrosetta.rosetta.core.kinematics.MoveMap method) get_branching_atoms2() (in module pyrosetta.rosetta.protocols.branch_angle) get_branching_residues() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_bridge_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) get_build_all_loops() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) get_build_attempts() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) get_build_ideal_geometry() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) get_build_site_only() (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_buildingblock_and_neighbor_subs() (in module pyrosetta.rosetta.core.pose.symmetry) get_bump_check() (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_bump_overlap_factor() (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) get_bumpcheck_atom_count_for_residue() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) get_bumpcheck_atoms_for_residue() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) get_c2f() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) get_c_axis() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_c_cyd_seqpos() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) get_c_most_segment() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment static method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment static method) get_C_term_DSSP() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) get_C_term_length() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) get_c_terminal_neighbor() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) get_c_terminal_parent() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) get_c_terminal_segment() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) get_ca_bfactors() (pyrosetta.rosetta.protocols.match.BfactorMPM method) get_CA_vectors() (in module pyrosetta.rosetta.core.scoring.dssp) get_CA_xyz() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) get_cacheable_cluster_data() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) get_CAcrd() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFrag method) get_calc_rot_freq() (pyrosetta.rosetta.core.pack.annealer.DebuggingAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FASTERAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbCoupledRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbLinkingRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbPwatSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.MultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.annealer.RotamerAssigningAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SequenceSymmetricAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SimAnnealerBase method) (pyrosetta.rosetta.core.pack.annealer.SmartFixbbSimAnnealer method) (pyrosetta.rosetta.protocols.flexpack.annealer.FlexbbSimAnnealer method) get_calculator() (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) get_calculator_name() (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) get_calphas() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) get_candidate_AAs() (in module pyrosetta.rosetta.protocols.recon_design) get_candidates() (pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_CompareTotalScore method) (pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) get_candidates_collector() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_carbohydrate_residues_and_tips_of_branch() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_carbohydrate_residues_of_branch() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_carbohydrate_tips_of_branch() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_CarbonHBondPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_cartesian() (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRelax method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRTMin method) get_cartesian_bonded_linear() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) get_cartesian_bonded_parameters() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) get_cartesian_bonded_skip_cutpoints() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) get_cav_approx() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) get_cavities() (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) get_cavity_positions() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) get_CB_Vecs_from_map() (in module pyrosetta.rosetta.protocols.sic_dock) get_CB_Vecs_from_pose() (in module pyrosetta.rosetta.protocols.sic_dock) get_ccd_closure_exist() (pyrosetta.rosetta.protocols.LoopRebuild method) get_cdr_bool_from_tag() (in module pyrosetta.rosetta.protocols.antibody) get_CDR_chain() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_CDR_cluster() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cdr_cluster() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher method) get_cdr_cluster_enum_manager() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_CDR_cluster_set() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cdr_design_options() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) get_CDR_end() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_CDR_end_PDB_num() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cdr_enum_for_cluster() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_CDR_in_loopsop() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_CDR_length() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_CDR_loop() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cdr_loop_with_overhang() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) get_cdr_loops() (in module pyrosetta.rosetta.protocols.antibody) get_CDR_loops() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cdr_loops() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) get_cdr_loops_with_overhang() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) get_CDR_name() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_CDR_name_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cdr_pdb_pos_from_input_pose() (in module pyrosetta.rosetta.protocols.tcr) get_cdr_sequence() (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) get_CDR_sequence_with_stem() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cdr_set_options() (in module pyrosetta.rosetta.protocols.antibody.design) get_CDR_start() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_CDR_start_PDB_num() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_CDRNameEnum_of_residue() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cdrs_movemap_with_overhang() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) get_cellDimensions() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) get_cen_deviation() (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) get_cen_dist() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_cen_scorefxn() (in module pyrosetta.rosetta.protocols.loops) get_CENcrd() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFrag method) get_CenHBPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_cenlist_from_pose() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) get_cenrot_library_by_aa() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary method) get_CenRotEnvPairPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_center() (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.pockets.SmallMol method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid method) get_center_ndx() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) get_center_of_mass() (in module pyrosetta.rosetta.core.pose) get_center_resnumber() (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) get_central_residues() (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) get_central_residues_in_each_of_two_edge_strands() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_central_residues_in_other_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_central_residues_in_this_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_centroid_data() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_centroid_dG() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_centroid_pose() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) get_centroid_scorefunction() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_centroid_scorefunction_min() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_CentroidDisulfidePotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_chain() (in module pyrosetta.rosetta.core.import_pose) (pyrosetta.rosetta.core.io.nmr.AtomSelection method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid method) get_chain_and_z() (in module pyrosetta.rosetta.protocols.membrane) get_chain_B_resNum() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_chain_break_tolerance() (pyrosetta.rosetta.protocols.LoopRebuild method) get_chain_connections() (in module pyrosetta.rosetta.core.pose.full_model_info) get_chain_for_full_model_resnum() (in module pyrosetta.rosetta.core.pose.full_model_info) get_chain_for_resnum() (in module pyrosetta.rosetta.core.pose.full_model_info) get_chain_from_chain_id() (in module pyrosetta.rosetta.core.pose) get_chain_from_jump_id() (in module pyrosetta.rosetta.core.pose) get_chain_groups() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_chain_id() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) get_chain_id_from_chain() (in module pyrosetta.rosetta.core.pose) get_chain_id_from_jump_id() (in module pyrosetta.rosetta.core.pose) get_chain_id_string() (in module pyrosetta.rosetta.core.conformation.symmetry) get_chain_ids_from_chain() (in module pyrosetta.rosetta.core.pose) get_chain_ids_from_chains() (in module pyrosetta.rosetta.core.pose) get_chain_residues() (in module pyrosetta.rosetta.core.pose) get_chain_to_degrease() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) get_chain_to_modify() (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) get_chainbreak_scores() (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) get_chainbreak_weight() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_chains() (in module pyrosetta.rosetta.core.pose) get_chains_from_cutpoint_open() (in module pyrosetta.rosetta.core.pose.full_model_info) get_chains_from_pdb_info() (in module pyrosetta.rosetta.core.pose.full_model_info) get_chains_full() (in module pyrosetta.rosetta.core.pose.full_model_info) get_charge() (pyrosetta.rosetta.core.io.nmr.ParaIon method) get_charged_residues_map() (pyrosetta.rosetta.core.energy_methods.PBLifetimeCache method) get_cheating_frags() (in module pyrosetta.rosetta.protocols.frags) (pyrosetta.rosetta.protocols.frags.VallData method) get_checkpoint_recoveries() (pyrosetta.rosetta.protocols.checkpoint.CheckPointer method) get_checkpoints() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover 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_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) get_chemical_edges() (pyrosetta.rosetta.core.kinematics.FoldTree method) get_chemical_name() (pyrosetta.rosetta.core.chemical.Element method) get_chemical_root_and_anchor_atomnos() (in module pyrosetta.rosetta.core.conformation) get_chemical_symbol() (pyrosetta.rosetta.core.chemical.Element method) get_chi() (pyrosetta.rosetta.core.kinematics.MoveMap method) get_chi_data() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_CHI_energy_function_linkage_type_for_phi_for_residue_in_pose() (in module pyrosetta.rosetta.core.scoring.carbohydrates) get_CHI_energy_function_linkage_type_for_psi_for_residue_in_pose() (in module pyrosetta.rosetta.core.scoring.carbohydrates) get_CHI_energy_function_linkage_type_for_residue_in_pose() (in module pyrosetta.rosetta.core.scoring.carbohydrates) get_chi_xx() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor method) get_chi_xy() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor method) get_chi_xz() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor method) get_chi_yy() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor method) get_chi_yz() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor method) get_chi_zz() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor method) get_CHIEnergyFunction() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_children() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) get_children_names() (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) get_chiral_residue_type() (in module pyrosetta.rosetta.protocols.simple_moves.chiral) get_chirality_sign() (in module pyrosetta.rosetta.core.io.pose_from_sfr) get_chis() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSewingResidue method) get_choice_min_and_max() (in module pyrosetta.rosetta.utility.xsd_util) get_chunk() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) get_chunk_size() (pyrosetta.rosetta.utility.sql_database.session method) get_cid() (pyrosetta.rosetta.protocols.constel.ChainTerm method) get_citation_by_doi() (pyrosetta.rosetta.basic.citation_manager.CitationManager method) get_citation_humanreadable() (pyrosetta.rosetta.core.pack.palette.PackerPaletteFactory method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationFactory method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorFactory method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricFactory method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorFactory method) (pyrosetta.rosetta.protocols.filters.FilterFactory method) (pyrosetta.rosetta.protocols.moves.MoverFactory method) get_citations_formatted() (pyrosetta.rosetta.basic.citation_manager.CitationCollection method) get_clash_checking() (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) get_clash_radius() (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.sewing.requirements.ClashRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandClashRequirement method) get_clash_score() (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch method) get_clash_score_from_pose() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) get_cloned_aa_comp_setup_helpers() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_cloned_mhc_epitope_setup_helpers() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_cloned_netcharge_setup_helpers() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_cloned_saved_pose() (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) get_closest_chain_ending() (in module pyrosetta.rosetta.protocols.denovo_design.components) get_closest_cluster() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher method) get_closest_distance_between_strands() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_closest_non_hoh_contact() (in module pyrosetta.rosetta.protocols.magnesium) get_closest_orbital_axis() (in module pyrosetta.rosetta.core.scoring.magnesium) get_closest_rotamer() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) get_closest_sequence_at_res() (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) get_closest_sequences() (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) get_closest_sister() (in module pyrosetta.rosetta.core.io.pose_from_sfr) get_closure_attempts() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) get_closure_solution() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) get_cluster() (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) get_cluster_center() (pyrosetta.rosetta.protocols.cluster.Cluster method) get_cluster_data() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) get_cluster_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cluster_for() (pyrosetta.rosetta.protocols.cluster.APCluster method) get_cluster_from_cache_or_ab_info() (in module pyrosetta.rosetta.protocols.antibody.clusters) get_cluster_length() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cluster_list() (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) get_cluster_name() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_cluster_name_by_PDB() (pyrosetta.rosetta.protocols.splice.SpliceSegment method) get_cluster_num() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_cluster_profile_probability_data() (in module pyrosetta.rosetta.protocols.antibody.design) get_cluster_radius() (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) get_clusterCenter() (pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster method) get_co_substrate() (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) get_code() (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel method) get_codes_from_saccharide_consensus_sequence() (in module pyrosetta.rosetta.core.enzymes) get_coeff() (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter method) get_col() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) get_column_name() (pyrosetta.rosetta.basic.database.insert_statement_generator.RowDataBase method) get_combine_if_fail_exist() (pyrosetta.rosetta.protocols.LoopRebuild method) get_comment() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) get_complex_energy() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_complexed_sasa() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_component() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) get_component_bounds() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) get_component_by_name() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) get_component_file() (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) get_component_lower_bound() (in module pyrosetta.rosetta.core.pose.symmetry) (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) get_component_of_residue() (in module pyrosetta.rosetta.core.pose.symmetry) (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) get_component_upper_bound() (in module pyrosetta.rosetta.core.pose.symmetry) (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) get_components() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) get_composite_real_metric_data() (pyrosetta.rosetta.core.simple_metrics.SimpleMetricData method) get_composite_string_metric_data() (pyrosetta.rosetta.core.simple_metrics.SimpleMetricData method) get_comprehensive_assembly_string() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) get_comprehensive_forward_assembly() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) get_comprehensive_reverse_assembly() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) get_computation_type() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) get_computed() (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) get_conformation_to_turn_type_map() (pyrosetta.rosetta.protocols.features.BetaTurnDetection static method) get_conformer() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) get_conformer_cen() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) get_conformer_switch_probability() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_conformer_table() (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelEnsemble method) get_connection_domains() (in module pyrosetta.rosetta.core.pose.full_model_info) get_connection_number() (in module pyrosetta.rosetta.core.chemical) get_connectivity_annotation_info() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) get_connolly_eggshell() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) get_connolly_eggshell_on_grid() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) get_connolly_surfacePoints() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) get_connolly_surfacePoints_within_grid() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) get_consensus_residues() (pyrosetta.rosetta.core.enzymes.EnzymeManager static method) get_consensus_sequence() (pyrosetta.rosetta.core.enzymes.EnzymeManager static method) get_consensus_sequence_type() (pyrosetta.rosetta.core.enzymes.EnzymeManager static method) get_conserved_residue_list() (in module pyrosetta.rosetta.protocols.antibody) get_const_atom_vector() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSewingResidue method) get_const_deer_data() (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) get_const_EnzConstraintIO_for_cstfile() (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts static method) get_const_job_node() (pyrosetta.rosetta.protocols.jd3.JobGenealogist method) get_const_options() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint method) get_const_owned_ligand_residues() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) get_const_ptr() (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.DataCache_basic_datacache_CacheableData_t method) (pyrosetta.rosetta.basic.datacache.DataCache_CacheableData method) (pyrosetta.rosetta.basic.datacache.DataCache_core_pose_datacache_CacheableObserver_t method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) get_const_reference_segment() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) get_const_residue_vector() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) get_constrain() (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) get_constrain_to_closest() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_constrainable_atoms_map() (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) get_constrained_atom_id() (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) get_constrained_atom_name() (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) get_constrained_lig_atoms() (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) get_constraint_for_target_state() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) get_constraint_weight() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) get_constraints_file() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) get_constraints_from_file() (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) get_constraints_from_link_records() (in module pyrosetta.rosetta.core.pose) get_constraints_from_pose() (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) get_constraints_only() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) get_contact() (pyrosetta.rosetta.protocols.contact_map.ContactMap method) get_contact_distance_cutoff() (pyrosetta.rosetta.protocols.sewing.requirements.KeepLigandContactsRequirement method) get_contact_resnum_string() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_contact_resnums_string() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) get_contact_selector() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) get_containing_helix_index() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments method) get_continuous_models_from_db() (in module pyrosetta.rosetta.protocols.legacy_sewing) get_coordinates() (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelAtom method) (pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint method) (pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint_AA method) (pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint method) (pyrosetta.rosetta.protocols.pockets.SmallMol method) get_coords_for_clash_check() (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) get_core_residues() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_core_selector() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_corresponding_residue_in_current() (pyrosetta.rosetta.core.id.SequenceMapping method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) get_cos_angle_to_closest_orbital_axis() (in module pyrosetta.rosetta.core.scoring.magnesium) get_cos_theta() (in module pyrosetta.rosetta.core.scoring.magnesium) get_count_pair_data_for_residue() (pyrosetta.rosetta.core.scoring.trie.RotamerTrieBase method) get_count_pair_function() (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) get_count_pair_function_trie() (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) get_countpair_representative_atom() (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) get_cp_rep_map_byname() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_cps() (pyrosetta.rosetta.protocols.constel.ChainTerm method) get_creator() (pyrosetta.rosetta.core.io.silent.SilentStructFactory method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintFactory method) (pyrosetta.rosetta.core.sequence.SequenceFactory method) get_crick_parameters() (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) get_crick_params_filename_formatted() (in module pyrosetta.rosetta.protocols.helical_bundle) get_crosslinker_enum() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover static method) get_crosslinker_name() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover static method) get_crossterm_interface_energy() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_crossterm_interface_energy_ratio() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_CSA_data() (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) get_cst_fa_file_option() (in module pyrosetta.rosetta.core.scoring.constraints) get_cst_factory() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO static method) get_cst_file_name() (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) get_cst_file_option() (in module pyrosetta.rosetta.core.scoring.constraints) get_cst_names() (pyrosetta.rosetta.core.scoring.constraints.ConstraintFactory method) get_cst_weight() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) get_Cstem_foldtree() (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) get_cstyle_A() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide method) get_cstyle_b() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide method) get_cstyle_b_individual_scale() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide method) get_Cter_loop_end() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) get_cterm_insert_flexibility() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) get_cterm_scaffold_flexibility() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) get_cterminal_peptide_bond_reference_frame() (in module pyrosetta.rosetta.core.pose.motif) get_cterminal_peptide_bond_reference_frame_atomids() (in module pyrosetta.rosetta.core.pose.motif) get_cube() (pyrosetta.rosetta.core.scoring.packstat.Octree2D method) get_cur_ncluster() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) get_curr_state_energy_following_partial_state_assignment() (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) get_curr_state_recent_state_id() (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) get_curr_upper_hbond_energies() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) get_current() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) get_current_AntibodyNumberingScheme() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_current_batch() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.BOINCJobDistributor method) (pyrosetta.rosetta.protocols.jd2.FileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.JobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.ShuffleFileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.VectorPoseJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor method) get_current_bs_id_and_closest_edge_bs_id_in_different_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_current_CDRDefinition() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_current_confnum() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) get_current_conformer() (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) get_current_conformer_ensemble1() (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) get_current_conformer_ensemble2() (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) get_current_contacts() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) get_current_cycle() (pyrosetta.rosetta.protocols.features.TrajectoryMapFeatures method) get_current_date() (in module pyrosetta.rosetta.utility) get_current_default_score_function_name() (in module pyrosetta.rosetta.core.scoring) get_current_energy() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge method) get_current_ensemble_size() (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel method) get_current_eqxyz() (pyrosetta.rosetta.protocols.md.CartesianMD method) get_current_for_node() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) get_current_global_sequence() (in module pyrosetta.rosetta.core.pose.full_model_info) get_current_job() (in module pyrosetta.rosetta.protocols.jd2) (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop 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.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder 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.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover 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.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover 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.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize 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.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.forge.components.BDR 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.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) (pyrosetta.rosetta.protocols.hydrate.Hydrate method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover 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.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM 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_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover 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.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover 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.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DsspMover method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.Mover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover 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.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot 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.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop 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.PrepackMover 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.SecretionOptimizationMover 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.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover 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.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover 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.IdealizeHelicesMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax 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.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover 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.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover 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_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover 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.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover 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.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover 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.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.star.StarAbinitio 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.SideChainCopier method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler 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.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover 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.monte_carlo.StepWiseMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) get_current_jobs_starting_pose() (in module pyrosetta.rosetta.protocols.jd2) get_current_jump() (pyrosetta.rosetta.protocols.symmetry.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SymmetrySlider method) get_current_network_state() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) get_current_output_tag() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) get_current_probabilities() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric static method) get_current_ref() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) get_current_seg() (pyrosetta.rosetta.protocols.splice.Splice method) get_current_state() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) get_current_state_for_node() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) get_current_structure_count() (in module pyrosetta.rosetta.protocols.features) get_current_tag() (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop 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.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder 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.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover 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.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover 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.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize 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.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.forge.components.BDR 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.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) (pyrosetta.rosetta.protocols.hydrate.Hydrate method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover 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.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM 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_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover 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.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover 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.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DsspMover method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.Mover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover 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.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot 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.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop 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.PrepackMover 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.SecretionOptimizationMover 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.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover 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.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover 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.IdealizeHelicesMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax 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.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover 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.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover 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_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover 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.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover 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.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover 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.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.star.StarAbinitio 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.SideChainCopier method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler 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.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover 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.monte_carlo.StepWiseMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) get_current_two_body_energy() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) get_custom_rama_table_filename() (pyrosetta.rosetta.core.scoring.Ramachandran method) get_custom_type() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric method) (pyrosetta.rosetta.protocols.filters.FilterValueMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric method) get_cutoff() (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff method) get_cutoff_angle() (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorer method) get_cutoff_distance() (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorer method) get_cutoff_squared() (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff method) get_cutpoint() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) get_cutpoint_closed() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_cutpoint_open_from_chains() (in module pyrosetta.rosetta.core.pose.full_model_info) get_cutpoints() (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) get_cutpoints_closed() (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) get_cycle_counts() (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) get_cyclic_pose_residue_mappings_from_selectors() (in module pyrosetta.rosetta.core.select.residue_selector) get_cyclization_name_from_type() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication static method) get_cyclization_type_from_name() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication static method) get_d2_low() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) get_D_equivalent() (in module pyrosetta.rosetta.core.chemical) get_d_equivalent() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_Da() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) get_data() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) (pyrosetta.rosetta.core.scoring.ResPairMinimizationData method) (pyrosetta.rosetta.core.scoring.ResSingleMinimizationData method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.frag_picker.JCouplingIO method) get_data_int() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) get_data_ndx() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) get_data_real() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) get_data_ref() (pyrosetta.rosetta.core.scoring.ResPairMinimizationData method) (pyrosetta.rosetta.core.scoring.ResSingleMinimizationData method) get_data_score() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) get_data_str() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) get_database() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase static method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorExternal method) get_database_name() (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) get_database_pq_schema() (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) get_DatabaseOccSolEne() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_dataset_name() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingleSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingleSet method) get_DB_filter_ptr() (in module pyrosetta.rosetta.protocols.features) get_db_mode() (pyrosetta.rosetta.utility.sql_database.session method) get_db_name() (pyrosetta.rosetta.utility.sql_database.session method) get_db_partition() (pyrosetta.rosetta.utility.sql_database.session method) get_db_session() (in module pyrosetta.rosetta.basic.database) (pyrosetta.rosetta.utility.sql_database.DatabaseSessionManager method) get_DC_data() (pyrosetta.rosetta.core.scoring.DipolarCoupling method) get_DC_data_type() (pyrosetta.rosetta.core.scoring.DC method) get_ddg_bisect_score() (pyrosetta.rosetta.protocols.simple_ddg.SSElementBisectddGFilter method) get_DDPLookupTable() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_debug() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) get_debug_rmsd() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.raw_data.DecoyStruct method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructJSON method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) get_deer_data() (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) get_default_bonus() (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) get_default_bridge_type() (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilter method) get_default_task_factory() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) get_definite_terminal_root() (in module pyrosetta.rosetta.core.pose) get_delete_interface_native_sidechains() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) get_delete_probability() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_DELPHI_espGrid_values() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) get_delta() (pyrosetta.rosetta.numeric.interpolation.spline.CubicSpline method) get_delta_energy_components() (pyrosetta.rosetta.protocols.ddg.ddGMover method) get_delta_magnetic_anisotropy_deriv() (in module pyrosetta.rosetta.core.scoring.rna.chemical_shift) get_delta_X_xx() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor method) get_delta_X_yy() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor method) get_delta_X_zz() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor method) get_deltaE_for_neighbor_following_perturbation() (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) get_deltaE_for_perturbation() (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) get_deltaE_for_relaxed_state_following_perturbation() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) get_den_fit_metric() (pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector method) get_density() (pyrosetta.rosetta.protocols.loop_grower.DensSkeleton method) get_density_map() (in module pyrosetta.rosetta.core.scoring.electron_density_atomwise) get_density_sc_scale_byres() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) get_deriv() (pyrosetta.rosetta.core.scoring.rna.TNA_SuitePotential method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_1_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_2_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_3_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_4_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_5_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_6_t method) get_deriv_count() (pyrosetta.rosetta.core.optimization.func_1d method) get_derivative() (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.SixDTransRotPotential method) (pyrosetta.rosetta.core.scoring.OneDDistPotential method) get_derivs_from_cycle() (in module pyrosetta.rosetta.core.scoring.power_diagram) get_derivs_from_cycles() (in module pyrosetta.rosetta.core.scoring.power_diagram) get_description() (pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop method) get_descriptor() (pyrosetta.rosetta.core.chemical.ElectronConfiguration static method) get_design() (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) get_design_positions() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) get_design_sequence_motif_syntax() (in module pyrosetta.rosetta.core.sequence) get_designable_residues() (in module pyrosetta.rosetta.protocols.recon_design) (pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesSeqRecoveryCache method) get_designable_sequence() (in module pyrosetta.rosetta.protocols.recon_design) get_desired_loops_exist() (pyrosetta.rosetta.protocols.LoopRebuild method) get_detect_interface() (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) get_deviation() (in module pyrosetta.rosetta.protocols.loops.loop_closure.ccd) get_DFIRE_potential() (in module pyrosetta.rosetta.core.scoring.methods.dfire) get_dG_ins_threshold() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) get_dG_tolerance() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) get_dihedral_angle() (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) get_dihedral_pattern() (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) get_dihedrals() (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) get_dimensions() (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid method) get_DirectReadoutPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_disabled() (pyrosetta.rosetta.protocols.checkpoint.CheckPointer method) get_discontinuous_models_from_db() (in module pyrosetta.rosetta.protocols.legacy_sewing) get_dist() (pyrosetta.rosetta.protocols.nmr.pre.PREDistanceRecord method) (pyrosetta.rosetta.protocols.pockets.UnionEdge method) get_dist_bins() (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) get_dist_cutoff() (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) get_dist_cutoff_multiplier() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) get_dist_err() (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) get_distance() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) get_distance_center_to_atom1() (pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch method) get_distance_cutoff() (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) get_distance_measure() (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) get_distance_potential_histogram_file() (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel method) get_distance_to_nth_shift() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.DsspShiftArray method) get_distance_to_start() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_distances() (in module pyrosetta.rosetta.core.membrane) get_distinct_sheet_id_from_sheet_table() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_distinct_sw_id_from_sandwich_table() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_distribution() (in module pyrosetta.rosetta.protocols.ligand_docking) get_disulf_file() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) get_disulf_jump() (pyrosetta.rosetta.protocols.splice.RBOutMover method) get_disulf_partner() (in module pyrosetta.rosetta.core.conformation) get_disulfide_atom_name() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) get_disulfide_derivatives() (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfidePotential method) get_disulfide_derivatives_old() (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfidePotential method) get_DisulfideMatchingPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_Dmax() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) get_dna_a_path() (pyrosetta.rosetta.protocols.dna_dock.DNAClashCheckFilter method) get_dna_b_path() (pyrosetta.rosetta.protocols.dna_dock.DNAClashCheckFilter method) get_DNA_backbone_bin() (in module pyrosetta.rosetta.core.scoring.dna) get_DNA_BasePotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_DNA_DihedralPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_DNA_EnvPairPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_DNABFormPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_DNATorsionPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_dock_chains() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) get_dock_chains_from_ab_dock_chains() (in module pyrosetta.rosetta.protocols.antibody.design) get_docking_foldtree() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) get_dof() (pyrosetta.rosetta.core.pack.dunbrack.MainchainTorsionReporter method) (pyrosetta.rosetta.core.pack.dunbrack.PeptideTorsionReporter method) (pyrosetta.rosetta.core.pack.dunbrack.PeptoidGeneralDOFReporter method) (pyrosetta.rosetta.core.pack.dunbrack.PeptoidOmegaReporter method) (pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter method) get_DOF() (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) get_dof_axis_and_end_pos() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) get_dof_derivative_weight() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) get_dof_id() (pyrosetta.rosetta.core.optimization.CartesianMinimizerMap method) get_dofs() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) get_dofs_from_energy_map() (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) get_dofs_pdb_name() (pyrosetta.rosetta.protocols.splice.Splice method) get_domain() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) get_domain_boundary_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_domain_boundary_suites() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_dome_water() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) get_donor_acceptor_group_from_heavyatom_index() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) get_dot_covered() (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) get_downstream_chain() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) get_downstream_connections() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) get_downstream_residue_that_this_torsion_moves() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_ds_atom_ids_needed() (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) get_dsbuilder() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) get_dsecox() (pyrosetta.rosetta.numeric.interpolation.spline.BicubicSpline method) (pyrosetta.rosetta.numeric.interpolation.spline.CubicSpline method) (pyrosetta.rosetta.numeric.interpolation.spline.TricubicSpline method) get_dsecoxy() (pyrosetta.rosetta.numeric.interpolation.spline.BicubicSpline method) (pyrosetta.rosetta.numeric.interpolation.spline.TricubicSpline method) get_dsecoxyz() (pyrosetta.rosetta.numeric.interpolation.spline.TricubicSpline method) get_dsecoxz() (pyrosetta.rosetta.numeric.interpolation.spline.TricubicSpline method) get_dsecoy() (pyrosetta.rosetta.numeric.interpolation.spline.BicubicSpline method) (pyrosetta.rosetta.numeric.interpolation.spline.TricubicSpline method) get_dsecoyz() (pyrosetta.rosetta.numeric.interpolation.spline.TricubicSpline method) get_dsecoz() (pyrosetta.rosetta.numeric.interpolation.spline.TricubicSpline method) get_dssp_code() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) (pyrosetta.rosetta.protocols.sewing.requirements.DsspSpecificLengthRequirement method) get_dssp_plus_abego_L_def() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) get_dssp_reduced_IG_as_L_secstruct() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) get_dssp_secstruct() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) get_dssp_unreduced_secstruct() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) get_dummy_ensemble() (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel method) get_dummy_rotation_matrix() (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) get_dump_dir() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) get_dump_multis() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) get_dump_singles() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) get_dun02_aa_parameters() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet static method) get_dun10_aa_parameters() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet static method) get_dw_dr() (pyrosetta.rosetta.core.energy_methods.FAElecContextData method) get_dwell_times() (pyrosetta.rosetta.core.pack.annealer.FixbbPwatSimAnnealer method) get_dynamic_scale() (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) get_E_haro_one_way() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) get_E_hpol_one_way() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) get_edens_stats_table() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_edge() (pyrosetta.rosetta.core.conformation.PointGraphPy method) (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) (pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) (pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) get_edge_exists() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintGraph method) (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.jd3.JobDigraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t method) get_edge_file_name() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_edge_from_char() (in module pyrosetta.rosetta.core.chemical.rna) get_edge_from_num() (in module pyrosetta.rosetta.core.chemical.rna) get_edge_map_generator() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_edge_memory_usage() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) get_edge_reweight() (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter method) (pyrosetta.rosetta.protocols.toolbox.IGInterfaceEdgeUpweighter method) (pyrosetta.rosetta.protocols.toolbox.IGLigandDesignEdgeUpweighter method) (pyrosetta.rosetta.protocols.toolbox.ResidueGroupIGEdgeUpweighter method) get_edge_table_ptr() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) get_edge_weight() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) get_effective_radii() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) get_efficiency() (pyrosetta.rosetta.core.enzymes.EnzymeManager static method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) get_eggshell_distance() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) get_Eig_xx() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) get_Eig_yy() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) get_Eig_zz() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) get_eigval() (pyrosetta.rosetta.protocols.normalmode.NormalMode method) get_eigvec_cart() (pyrosetta.rosetta.protocols.normalmode.NormalMode method) get_eigvec_tor() (pyrosetta.rosetta.protocols.normalmode.NormalMode method) get_elec_scale() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) get_electron_affinity() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_electron_configuration() (pyrosetta.rosetta.core.chemical.Element method) get_electronegativity() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_electrostatics_energy() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) get_element_type() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_embedded_residue_selector() (in module pyrosetta.rosetta.core.select.residue_selector) get_end() (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFragment method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandFragment method) get_end2() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) get_end_res() (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) get_end_temperature() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_ending_residue() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseSegment method) GET_ENERGIES (pyrosetta.rosetta.basic.ProfTag attribute) get_energies_map_from_scored_pose() (pyrosetta.rosetta.core.io.raw_data.ScoreMap static method) get_energy() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_energy_current_state_assignment() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) get_energy_following_partial_state_assignment() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) get_energy_following_relaxation() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) get_energy_for_alt_state() (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) get_energy_for_perturbed_state() (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) get_energy_map() (pyrosetta.rosetta.protocols.relax.EnergyMapContainer method) get_energy_map_from_dofs() (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) get_energy_node() (pyrosetta.rosetta.core.scoring.EnergyGraph method) get_energy_PD_current_state_assignment() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) get_energy_state() (pyrosetta.rosetta.core.energy_methods.PBLifetimeCache method) get_energy_sum_for_vertex_group() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) get_enforce_bb_contiguity() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) get_ensemble() (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) get_ensemble_ca_rmsd() (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) get_ensemble_diversity() (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) get_ensemble_size() (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelEnsemble method) get_ensured_sites() (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) get_enumerated_module_type_name() (pyrosetta.rosetta.basic.citation_manager.CitationCollection static method) get_environment_dependent_weight() (in module pyrosetta.rosetta.core.scoring.hbonds) get_EnvPairPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_enzcst_io() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) get_enzdes_observer() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) get_enzyme() (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) get_enzyme_family() (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) get_epitope_residues() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) get_eps() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_eps_range() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_epsilon_torsions() (in module pyrosetta.rosetta.core.chemical.rna) get_equiv() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerLinks method) (pyrosetta.rosetta.protocols.symmetry.NCSResMapping method) get_euler_angles() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) get_euler_convention() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) get_eval_count() (pyrosetta.rosetta.core.optimization.func_1d method) get_exact() (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) get_excluded_sites() (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) get_exemplar_for() (pyrosetta.rosetta.protocols.cluster.APCluster method) get_exp_val() (pyrosetta.rosetta.core.scoring.func.SplineFunc method) get_extend_existing_networks() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_extend_mode() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_extended() (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) get_extra() (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) get_extra_bodies() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) get_extra_bodies_chains() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) get_extra_cutpoints_from_names() (in module pyrosetta.rosetta.core.import_pose) get_extra_data() (pyrosetta.rosetta.protocols.loophash.BackboneDB method) get_f1_f2() (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.GaussianChainFuncPotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.LoopClosePotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.SixDTransRotPotentialEvaluator method) get_f2c() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) get_fa_rep_thresh() (pyrosetta.rosetta.protocols.dna_dock.DNAClashCheckFilter method) (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilter method) get_fa_score() (pyrosetta.rosetta.protocols.rpc.JSON_RPC method) get_fa_scorefxn() (in module pyrosetta.rosetta.protocols.loops) get_FACTSPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_fade_correction() (in module pyrosetta.rosetta.core.scoring.rna) get_far_c_terminal_parent() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment static method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment static method) get_far_n_terminal_parent() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment static method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment static method) get_favor_native_bonus() (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) get_features_reporter() (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) get_ff() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) get_field_strength() (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingleSet method) get_file_contents() (pyrosetta.rosetta.utility.io.FileContentsMap method) (pyrosetta.rosetta.utility.io.GeneralFileContents method) (pyrosetta.rosetta.utility.io.GeneralFileContentsVector method) (pyrosetta.rosetta.utility.io.GeneralFileManager method) (pyrosetta.rosetta.utility.io.GeneralFileManagerVector method) get_file_contents_ref() (pyrosetta.rosetta.utility.io.FileContentsMap method) get_file_lines() (pyrosetta.rosetta.protocols.relax.RelaxScriptFileContents method) get_file_name() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_file_option() (in module pyrosetta.rosetta.basic.options) get_file_vector_option() (in module pyrosetta.rosetta.basic.options) get_filename() (pyrosetta.rosetta.core.scoring.func.SplineFunc method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_per_lanthanides method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_per_lanthanides_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_per_lanthanides_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_per_lanthanides_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 method) get_filenames() (in module pyrosetta.rosetta.protocols.motifs) (pyrosetta.rosetta.core.import_pose.pose_stream.PDBPoseInputStream method) get_filter() (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects method) get_filter_by_phipsi() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) get_filter_names_from_xsd() (in module pyrosetta.rosetta.utility.xsd_util) get_filter_omega() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) get_filter_param() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) get_filter_SASA() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) get_filter_score() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) get_filter_status() (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) get_filter_type_by_name() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) get_filter_type_name() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) get_filtered_sheet_topology() (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilter method) get_filteronly_solutions() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) get_final_energy() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) get_final_fragments() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_final_pose() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) get_final_RMSD() (pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop method) get_final_sm_type() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric method) (pyrosetta.rosetta.protocols.filters.FilterValueMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric method) get_finalPoseOP() (pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop method) get_first() (pyrosetta.rosetta.core.scoring.packstat.trace method) get_first_atom() (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData method) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) get_first_index_in_query() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) get_first_index_in_vall() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) get_first_node_ind() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.TenANeighborEdge method) (pyrosetta.rosetta.core.scoring.TwelveANeighborEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) (pyrosetta.rosetta.utility.graph.Edge method) (pyrosetta.rosetta.utility.graph.LowMemEdge method) get_first_protein_residue() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) get_first_residue_id() (pyrosetta.rosetta.protocols.frag_picker.CSTalosIO method) (pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO method) get_fix_backbone() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_fixed_chains() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_fixed_domain_from_full_model_info_const() (in module pyrosetta.rosetta.core.pose.full_model_info) get_fixed_pt() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode method) get_fixed_res() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) get_flags() (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelector method) get_flexseg_bb_offset() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) get_flexseg_for_bb() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) get_fmax() (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) get_fmin() (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) get_fobj() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) get_fold_tree() (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) get_fold_tree_root() (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) get_folding_vertices() (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) get_FoldTree_AllCDRs() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_FoldTree_AllCDRs_LHDock() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_FoldTree_L_HA() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_FoldTree_LA_H() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_FoldTree_LH_A() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_foldtree_seqsep() (in module pyrosetta.rosetta.protocols.fldsgn.potentials.sspot) get_foldtree_which_partitions() (in module pyrosetta.rosetta.core.kinematics) get_forcefield() (in module pyrosetta.rosetta.core.chemical.rdkit) get_formal_charge() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_formatted_citation() (pyrosetta.rosetta.basic.citation_manager.Citation method) get_forward_assembly() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) get_fourth_atom() (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) get_fourth_offset() (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) get_fraction() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) get_frag3() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_frag_data() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) get_frag_energy_for_alt_bb_state() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) get_frag_energy_for_curr_bb_state_and_finalize_alt_energy_total() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) get_frag_factory() (pyrosetta.rosetta.core.fragment.FragmentIO method) get_frag_sizes() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_frag_weight_file() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) get_fragment_coordinates() (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore method) (pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore method) get_fragment_length() (pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore method) get_fragment_library_pointer() (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) (pyrosetta.rosetta.core.fragment.rna.RNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) get_fragment_lines() (pyrosetta.rosetta.core.fragment.rna.RNA_FragmentHomologyExclusion method) get_fragment_store() (pyrosetta.protocols.h5_fragment_store_provider.H5PyFragmentStoreProvider method) (pyrosetta.rosetta.protocols.indexed_structure_store.BinaryFragmentStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreProvider method) (pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore method) get_fragment_torsion() (pyrosetta.rosetta.core.fragment.rna.FragmentLibrary method) get_fragment_torsion_set() (pyrosetta.rosetta.core.fragment.rna.FragmentLibrary method) get_fragmentLookup() (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore method) get_fragments() (pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet method) get_fragments_by_CA_distances_and_NCpoints_restrains() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) get_frags() (in module pyrosetta.rosetta.protocols.frags) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.frags.RMSVallData method) (pyrosetta.rosetta.protocols.frags.VallData method) get_frame_ala() (in module pyrosetta.rosetta.core.pose.motif) get_frame_arg() (in module pyrosetta.rosetta.core.pose.motif) get_frame_asn() (in module pyrosetta.rosetta.core.pose.motif) get_frame_asp() (in module pyrosetta.rosetta.core.pose.motif) get_frame_cys() (in module pyrosetta.rosetta.core.pose.motif) get_frame_gln() (in module pyrosetta.rosetta.core.pose.motif) get_frame_glu() (in module pyrosetta.rosetta.core.pose.motif) get_frame_gly() (in module pyrosetta.rosetta.core.pose.motif) get_frame_his() (in module pyrosetta.rosetta.core.pose.motif) get_frame_ile() (in module pyrosetta.rosetta.core.pose.motif) get_frame_leu() (in module pyrosetta.rosetta.core.pose.motif) get_frame_lys() (in module pyrosetta.rosetta.core.pose.motif) get_frame_met() (in module pyrosetta.rosetta.core.pose.motif) get_frame_phe() (in module pyrosetta.rosetta.core.pose.motif) get_frame_pro() (in module pyrosetta.rosetta.core.pose.motif) get_frame_ser() (in module pyrosetta.rosetta.core.pose.motif) get_frame_thr() (in module pyrosetta.rosetta.core.pose.motif) get_frame_trp() (in module pyrosetta.rosetta.core.pose.motif) get_frame_tyr() (in module pyrosetta.rosetta.core.pose.motif) get_frame_val() (in module pyrosetta.rosetta.core.pose.motif) get_frequency() (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer method) get_from_const_pose() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) get_from_pose() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) get_fstyle_b() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_per_lanthanides method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_per_lanthanides_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_per_lanthanides_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_per_lanthanides_Ts4 method) get_full_edge_from_num() (in module pyrosetta.rosetta.core.chemical.rna) get_full_intracomponent_and_neighbor_resis() (in module pyrosetta.rosetta.core.pose.symmetry) get_full_intracomponent_and_neighbor_subpose() (in module pyrosetta.rosetta.core.pose.symmetry) get_full_intracomponent_and_neighbor_subs() (in module pyrosetta.rosetta.core.pose.symmetry) get_full_intracomponent_neighbor_resis() (in module pyrosetta.rosetta.core.pose.symmetry) get_full_intracomponent_neighbor_subpose() (in module pyrosetta.rosetta.core.pose.symmetry) get_full_intracomponent_neighbor_subs() (in module pyrosetta.rosetta.core.pose.symmetry) get_full_intracomponent_resis() (in module pyrosetta.rosetta.core.pose.symmetry) get_full_intracomponent_subpose() (in module pyrosetta.rosetta.core.pose.symmetry) get_full_intracomponent_subs() (in module pyrosetta.rosetta.core.pose.symmetry) get_full_LW_orientation_from_num() (in module pyrosetta.rosetta.core.chemical.rna) get_full_motif_bb_alignment_mode() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch method) get_full_orientation_from_num() (in module pyrosetta.rosetta.core.chemical.rna) get_full_packing_frequency() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) get_full_sequence() (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) get_full_side_from_num() (in module pyrosetta.rosetta.core.chemical.rna) get_full_torsions() (in module pyrosetta.rosetta.core.chemical.rna) get_full_type_name() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSewingResidue method) get_fullatom_pose() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) get_fullatom_scorefunction() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) get_FullatomDisulfidePotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_func() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomToAxisConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraint 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.FabConstraint method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedDihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueCouplingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.RTConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorer method) get_func_factory() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO static method) get_function() (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData method) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) get_function_names() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) get_G() (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) get_gamma() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) get_gaussian_deriv() (in module pyrosetta.rosetta.core.scoring.magnesium) get_gaussian_potential_score() (in module pyrosetta.rosetta.core.scoring.magnesium) get_gaussian_score() (in module pyrosetta.rosetta.core.scoring.magnesium) get_gdt() (in module pyrosetta.rosetta.protocols.electron_density) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) get_GDTHA() (pyrosetta.rosetta.core.scoring.TMscore method) get_gdtmm() (in module pyrosetta.rosetta.protocols.hybridization) get_GDTTS() (pyrosetta.rosetta.core.scoring.TMscore method) get_GenBornPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_GenericBondedPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_geometry_score_weight() (pyrosetta.rosetta.protocols.sewing.hashing.LigandBindingResPlacer method) get_gJ() (pyrosetta.rosetta.core.io.nmr.ParaIon method) get_global_coords_as_FArray2D() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) get_global_i() (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) get_global_requirement() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory method) get_gly_interface_energy() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_glycan_connecting_protein_branch_point() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_glycan_position_from_resnum() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_glycan_sampler_rounds() (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) get_glycan_start_points() (in module pyrosetta.rosetta.core.conformation.carbohydrates) get_glycan_tree_set() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) get_glycan_tree_size() (in module pyrosetta.rosetta.core.conformation.carbohydrates) get_GlycanDock_IAM() (in module pyrosetta.rosetta.protocols.glycan_docking) get_glycine_correction_for_node() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) get_glycolig_subset_with_torsions() (in module pyrosetta.rosetta.protocols.glycan_docking) get_glycosidic_bond_residues() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_glycosidic_torsion() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_glycosidic_TorsionIDs() (in module pyrosetta.rosetta.core.conformation.carbohydrates) get_glycosylation_residue() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) get_GOE_packstat_report() (pyrosetta.rosetta.protocols.vip.VIP_Report method) get_GOE_relaxed_report() (pyrosetta.rosetta.protocols.vip.VIP_Report method) get_GOE_repack_report() (pyrosetta.rosetta.protocols.vip.VIP_Report method) get_graft_design_options() (in module pyrosetta.rosetta.protocols.antibody.design) get_grid() (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid method) get_grid_all_atomtypes() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) get_grid_atom1() (pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch method) get_grid_atom2() (pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch method) get_grid_atom_name_1() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 method) get_grid_atom_name_2() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 method) get_grid_cone_angle_cutoff() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 method) get_grid_edge() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 method) get_grid_k_vector() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 method) get_grid_large_cutoff() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 method) get_grid_max_radius() (pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch method) get_grid_min_radius() (pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch method) get_grid_names() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) get_grid_residue_num_1() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 method) get_grid_residue_num_2() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 method) get_grid_search_center() (pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch method) get_grid_search_parameters() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameterManager method) get_grid_small_cutoff() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 method) get_grid_step() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 method) get_grids() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridManager method) get_gridsearch_iterator() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) get_gridsearch_range() (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) get_groove_widths() (in module pyrosetta.rosetta.core.scoring.dna) get_grow_attempts() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) get_GTPase_lys() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) get_H3_kink_type() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_H3_kink_type_name() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_HAdist() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) get_half_width() (pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction method) get_handedness_score_flag() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) get_hardsphere_bump_check() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) get_harmonic_ca_cst_std_dev() (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) get_hash_excluding_chain() (in module pyrosetta.rosetta.core.pose) get_hash_from_chain() (in module pyrosetta.rosetta.core.pose) get_hash_from_pos() (in module pyrosetta.rosetta.core.pose) get_hash_map_size() (pyrosetta.rosetta.protocols.sewing.hashing.Hasher method) get_hashed() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_hashed_fragment_store() (pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore method) get_hb_acc_chem_type() (in module pyrosetta.rosetta.core.scoring.hbonds) get_hb_don_chem_type() (in module pyrosetta.rosetta.core.scoring.hbonds) get_hb_e_cutoff() (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) get_hbe_acc_hybrid() (in module pyrosetta.rosetta.core.scoring.hbonds) get_hbond_atom_pairs() (in module pyrosetta.rosetta.protocols.hbnet) get_hbond_energies() (in module pyrosetta.rosetta.core.scoring.hbonds) get_hbond_energy_cutoff() (pyrosetta.rosetta.protocols.residue_selectors.HBondSelector method) get_hbond_score_weighted() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) get_hbond_weight_type() (in module pyrosetta.rosetta.core.scoring.hbonds) get_hbonds() (in module pyrosetta.bindings.pose) (pyrosetta.rosetta.core.pose.Pose method) get_head_node() (pyrosetta.rosetta.protocols.jd3.JobDirectedEdge method) (pyrosetta.rosetta.utility.graph.DirectedEdge method) get_head_node_ind() (pyrosetta.rosetta.protocols.jd3.JobDirectedEdge method) (pyrosetta.rosetta.utility.graph.DirectedEdge method) get_helical_params() (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) get_helix_end() (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) get_helix_ends() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) get_helix_id() (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_helix_pairings() (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing static method) get_helix_start() (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) get_highres_conformer_filter_type() (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel method) get_highres_scorefxn() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) get_hist() (pyrosetta.rosetta.protocols.recces.Histogram method) get_histogram_vector() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics method) get_history() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) get_home_dir() (in module pyrosetta.rosetta.utility.file) get_homogeneous_transform_com_from_orig() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch method) get_homologs() (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore method) get_hss_triplets() (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing static method) get_hybrid_orbital_type() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_hydration_stats() (in module pyrosetta.rosetta.protocols.magnesium) get_hydrogens_bonded_to_ring_atom() (pyrosetta.rosetta.core.conformation.Residue method) get_HydroxylTorsionPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_i() (pyrosetta.rosetta.core.scoring.packstat.Octree2D method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandFragment method) get_IAM() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) get_id() (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandFragment method) (pyrosetta.rosetta.protocols.frag_picker.scores.ABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) get_ideal_angle_about_contact() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_ideal_angle_about_metal() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_ideal_conformer_by_CP_parameters() (pyrosetta.rosetta.core.chemical.rings.RingConformerSet method) get_ideal_conformer_by_name() (pyrosetta.rosetta.core.chemical.rings.RingConformerSet method) get_ideal_conformer_from_nus() (pyrosetta.rosetta.core.chemical.rings.RingConformerSet method) get_ideal_contacts() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) get_ideal_dihedral_3() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_ideal_dihedral_about_contact() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_ideal_dihedral_about_metal() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_ideal_distance() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_ideal_hydrogenBond_atoms() (pyrosetta.rosetta.protocols.pockets.GenPharmacophore method) get_idealize_loop_first() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) get_idx() (in module pyrosetta.rosetta.core.scoring.rna.data) get_idx_for_other_pose() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) get_idx_for_other_pose_with_residue() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) get_idx_for_other_pose_with_residues() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) get_ignore_unrecognized_res() (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecovery method) get_importance() (pyrosetta.rosetta.protocols.normalmode.NormalMode method) get_incident_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NodeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) get_incident_otf_edge() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) get_incident_symmin_edge() (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) get_incident_symmlinmem_edge() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) get_include_backbone_atoms() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD method) get_include_bb_bb() (pyrosetta.rosetta.protocols.residue_selectors.HBondSelector method) get_include_focus() (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector method) get_include_only_end() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter method) get_include_only_start() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter method) get_include_subunit() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_incomplete_connections() (in module pyrosetta.rosetta.protocols.ligand_docking) get_ind_res() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_index() (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution method) get_index_in_vall() (pyrosetta.rosetta.core.fragment.rna.TorsionSet method) get_index_of_adjacent_node() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NodeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) get_index_of_last_mover_used() (pyrosetta.rosetta.protocols.moves.RandomMover method) get_index_to_vd() (pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler method) get_indices_of_moving_chunks() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) get_indices_of_voxel_from_coordinates() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) get_individual_scale() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter method) get_init() (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) get_init_value() (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) get_initial() (pyrosetta.rosetta.protocols.hybridization.TMalign method) get_initial_fgt() (pyrosetta.rosetta.protocols.hybridization.TMalign method) get_initial_job_dag_and_queue() (pyrosetta.rosetta.protocols.jd3.job_distributors.JobExtractor method) get_initial_local() (pyrosetta.rosetta.protocols.hybridization.TMalign method) get_initial_ss() (pyrosetta.rosetta.protocols.hybridization.TMalign method) get_initial_ssplus() (pyrosetta.rosetta.protocols.hybridization.TMalign method) get_inner_cycles() (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) get_inner_radius() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) get_inneriterations() (pyrosetta.rosetta.core.pack.annealer.DebuggingAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FASTERAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbCoupledRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbLinkingRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbPwatSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.MultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.annealer.RotamerAssigningAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SequenceSymmetricAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SimAnnealerBase method) (pyrosetta.rosetta.core.pack.annealer.SmartFixbbSimAnnealer method) (pyrosetta.rosetta.protocols.flexpack.annealer.FlexbbSimAnnealer method) get_inp_chi() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_input_data() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_manager_Ts4 method) get_input_domain_from_full_model_info_const() (in module pyrosetta.rosetta.core.pose.full_model_info) get_input_pose() (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop 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.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder 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.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover 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.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover 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.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize 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.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.forge.components.BDR 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.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) (pyrosetta.rosetta.protocols.hydrate.Hydrate method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover 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.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM 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_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover 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.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover 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.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DsspMover method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.Mover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover 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.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot 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.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop 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.PrepackMover 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.SecretionOptimizationMover 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.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover 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.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover 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.IdealizeHelicesMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax 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.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover 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.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover 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_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover 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.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover 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.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover 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.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.star.StarAbinitio 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.SideChainCopier method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler 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.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover 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.monte_carlo.StepWiseMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) get_input_poses_to_deallocate() (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJobTracker method) get_input_res() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) get_input_set_defined() (pyrosetta.rosetta.protocols.residue_selectors.HBondSelector method) get_input_set_selector() (pyrosetta.rosetta.protocols.residue_selectors.HBondSelector method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) get_input_set_str() (pyrosetta.rosetta.protocols.residue_selectors.HBondSelector method) get_input_streams() (pyrosetta.rosetta.core.import_pose.pose_stream.MetaPoseInputStream method) get_input_stub() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) get_instance() (pyrosetta.rosetta.basic.citation_manager.CitationManager static method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataFactory static method) (pyrosetta.rosetta.basic.mpi.MessageListenerFactory static method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory static method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory static method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory static method) (pyrosetta.rosetta.basic.sampling.orientations.QuaternionGridManager static method) (pyrosetta.rosetta.basic.tensorflow_manager.RosettaTensorflowManager static method) (pyrosetta.rosetta.basic.thread_manager.RosettaThreadManager static method) (pyrosetta.rosetta.basic.thread_manager.RosettaThreadManagerInitializationTracker static method) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager static method) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager static method) (pyrosetta.rosetta.core.chemical.ChemicalManager static method) (pyrosetta.rosetta.core.chemical.orbitals.OrbitalTypeMapper static method) (pyrosetta.rosetta.core.chemical.PatchOperationFactory static method) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager static method) (pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationFactory static method) (pyrosetta.rosetta.core.energy_methods.GridInfo static method) (pyrosetta.rosetta.core.energy_methods.WaterWeightGridSet static method) (pyrosetta.rosetta.core.enzymes.EnzymeManager static method) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager static method) (pyrosetta.rosetta.core.import_pose.libraries.RNA_LibraryManager static method) (pyrosetta.rosetta.core.io.nmr.ParamagneticDatabaseHandler static method) (pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseHandler static method) (pyrosetta.rosetta.core.io.NomenclatureManager static method) (pyrosetta.rosetta.core.io.pdb.RecordCollection static method) (pyrosetta.rosetta.core.io.silent.SilentStructFactory static method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary static method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapDatabase static method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData static method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential static method) (pyrosetta.rosetta.core.pack.palette.PackerPaletteFactory static method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryFactory static method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterFactory static method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory static method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationFactory static method) (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculatorManager static method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintFactory static method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO static method) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase static method) (pyrosetta.rosetta.core.scoring.motif.MotifHashManager static method) (pyrosetta.rosetta.core.scoring.nmr.NMRDataFactory static method) (pyrosetta.rosetta.core.scoring.saxs.SinXOverX static method) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory static method) (pyrosetta.rosetta.core.scoring.ScoringManager static method) (pyrosetta.rosetta.core.select.jump_selector.JumpSelectorFactory static method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorFactory static method) (pyrosetta.rosetta.core.sequence.SequenceFactory static method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricFactory static method) (pyrosetta.rosetta.numeric.model_quality.RmsData static method) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager static method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper static method) (pyrosetta.rosetta.protocols.chemistries.ChemistryFactory static method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorFactory static method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager static method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo static method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory static method) (pyrosetta.rosetta.protocols.denovo_design.components.Picker static method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory static method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDatabase static method) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory static method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLReferenceSDFilesManager static method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLSampleConfsManager static method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory static method) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory static method) (pyrosetta.rosetta.protocols.filters.FilterFactory static method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory static method) (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager static method) (pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreManager static method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor static method) (pyrosetta.rosetta.protocols.jd2.BOINCJobDistributor static method) (pyrosetta.rosetta.protocols.jd2.FileSystemJobDistributor static method) (pyrosetta.rosetta.protocols.jd2.JobDistributor static method) (pyrosetta.rosetta.protocols.jd2.JobInputterFactory static method) (pyrosetta.rosetta.protocols.jd2.JobOutputterFactory static method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor static method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor static method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor static method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor static method) (pyrosetta.rosetta.protocols.jd2.ShuffleFileSystemJobDistributor static method) (pyrosetta.rosetta.protocols.jd2.VectorPoseJobDistributor static method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputterFactory static method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputterFactory static method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterFactory static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory static method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary static method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary static method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory static method) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap static method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory static method) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory static method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory static method) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler static method) (pyrosetta.rosetta.protocols.moves.MoverFactory static method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricFactory static method) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance static method) (pyrosetta.rosetta.protocols.noesy_assign.MethylNameLibrary static method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters static method) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridFactory static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridManager static method) (pyrosetta.rosetta.protocols.relax.RelaxScriptManager static method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterFactory static method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorFactory static method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsSchemaValidator static method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory static method) (pyrosetta.rosetta.protocols.scoring.InterchainPotential static method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input_manager static method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager static method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManagerSingleton static method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameterManager static method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameterManager static method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenterManager static method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_manager_Ts1 static method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 static method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_manager_Ts2 static method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 static method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_manager_Ts3 static method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 static method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_manager_Ts4 static method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 static method) (pyrosetta.rosetta.protocols.sewing.requirements.AssemblyRequirementFactory static method) (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorerFactory static method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory static method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor static method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor static method) (pyrosetta.rosetta.utility.Inline_File_Provider static method) (pyrosetta.rosetta.utility.io.GeneralFileManager static method) (pyrosetta.rosetta.utility.io.GeneralFileManagerVector static method) (pyrosetta.rosetta.utility.SingletonBase_basic_citation_manager_CitationManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_basic_datacache_WriteableCacheableDataFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_basic_mpi_MessageListenerFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_basic_resource_manager_ResourceLoaderFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_basic_resource_manager_ResourceLocatorFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_basic_resource_manager_ResourceManagerFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_basic_sampling_orientations_QuaternionGridManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_basic_tensorflow_manager_RosettaTensorflowManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_basic_thread_manager_RosettaThreadManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_basic_thread_manager_RosettaThreadManagerInitializationTracker_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_chemical_AtomPropertiesManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_chemical_carbohydrates_CarbohydrateInfoManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_chemical_ChemicalManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_chemical_orbitals_OrbitalTypeMapper_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_chemical_PatchOperationFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_chemical_rings_RingConformerManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_chemical_rotamers_RotamerLibrarySpecificationFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_energy_methods_GridInfo_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_energy_methods_WaterWeightGridSet_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_enzymes_EnzymeManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_fragment_picking_old_FragmentLibraryManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_import_pose_libraries_RNA_LibraryManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_io_nmr_ParamagneticDatabaseHandler_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_io_nmr_SpinlabelDatabaseHandler_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_io_NomenclatureManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_io_pdb_RecordCollection_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_io_silent_SilentStructFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_pack_dunbrack_cenrot_CenrotLibrary_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_pack_dunbrack_RotamerLibrary_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_pack_guidance_scoreterms_sap_SapDatabase_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_pack_interaction_graph_RotamerDotsRadiusData_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_pack_interaction_graph_SurfacePotential_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_pack_palette_PackerPaletteFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_pack_rotamers_SingleResidueRotamerLibraryFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_pack_task_operation_ResFilterFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_pack_task_operation_ResLvlTaskOperationFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_pack_task_operation_TaskOperationFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_scoring_bin_transitions_BinTransitionCalculatorManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_scoring_constraints_ConstraintFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_scoring_constraints_ConstraintIO_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_scoring_lkball_LKBallDatabase_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_scoring_motif_MotifHashManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_scoring_nmr_NMRDataFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_scoring_saxs_SinXOverX_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_scoring_ScoreFunctionFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_scoring_ScoringManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_select_jump_selector_JumpSelectorFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_select_residue_selector_ResidueSelectorFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_sequence_SequenceFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_core_simple_metrics_SimpleMetricFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_numeric_model_quality_RmsData_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_antibody_grafting_RegExManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_antibody_grafting_SCS_Helper_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_chemistries_ChemistryFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_constraint_generator_ConstraintGeneratorFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_constraint_generator_ConstraintsManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_constraint_generator_HydrogenBondInfo_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_denovo_design_architects_DeNovoArchitectFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_denovo_design_components_Picker_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_denovo_design_components_StructureDataFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_denovo_design_task_operations_ConsensusLoopDatabase_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_docking_DockingHighResFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_drug_design_bcl_BCLReferenceSDFilesManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_drug_design_bcl_BCLSampleConfsManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_evaluation_EvaluatorFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_features_FeaturesReporterFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_filters_FilterFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_genetic_algorithm_EntityElementFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_indexed_structure_store_FragmentStoreManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_indexed_structure_store_StructureStoreManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_jd2_JobInputterFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_jd2_JobOutputterFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_jd3_chunk_library_inputters_ChunkLibraryInputterFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_jd3_full_model_inputters_FullModelInputterFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_jd3_pose_inputters_PoseInputterFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_jd3_pose_outputters_PoseOutputterFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_jumping_StandardDisulfPairingLibrary_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_jumping_StandardPairingLibrary_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_legacy_sewing_sampling_requirements_LegacyRequirementFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_ligand_docking_DistributionMap_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_ligand_docking_rdf_RDFFunctionFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_loops_loop_mover_refine_LoopRefineInnerCycleFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_loops_LoopMoverFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_loops_loops_definers_LoopsDefinerFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_matdes_SymDofMoverSampler_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_moves_MoverFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_multistage_rosetta_scripts_cluster_ClusterMetricFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_noesy_assign_CovalentCompliance_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_noesy_assign_MethylNameLibrary_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_parser_DataLoaderFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_qsar_scoring_grid_GridFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_qsar_scoring_grid_GridManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_relax_RelaxScriptManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_rosetta_scripts_PosePropertyReporterFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_rosetta_scripts_PoseSelectorFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_rosetta_scripts_RosettaScriptsSchemaValidator_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_rotamer_recovery_RotamerRecoveryFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_InterchainPotential_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_methods_pcs2_PcsDataCenterManagerSingleton_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_methods_pcs2_PcsEnergyParameterManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_methods_pcs2_PcsGridSearchParameterManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_methods_pcs2_PcsInputCenterManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_methods_pcs_PCS_data_input_manager_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_methods_pcs_PCS_Energy_parameters_manager_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_methods_pcsTs1_PCS_Energy_parameters_manager_Ts1_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_methods_pcsTs2_PCS_Energy_parameters_manager_Ts2_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_methods_pcsTs3_PCS_Energy_parameters_manager_Ts3_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_methods_pcsTs4_PCS_Energy_parameters_manager_Ts4_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_sewing_requirements_AssemblyRequirementFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_sewing_scoring_AssemblyScorerFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_protocols_topology_broker_TopologyClaimerFactory_t static method) (pyrosetta.rosetta.utility.SingletonBase_utility_Inline_File_Provider_t static method) (pyrosetta.rosetta.utility.SingletonBase_utility_io_GeneralFileManager_t static method) (pyrosetta.rosetta.utility.SingletonBase_utility_io_GeneralFileManagerVector_t static method) (pyrosetta.rosetta.utility.SingletonBase_utility_sql_database_DatabaseSessionManager_t static method) (pyrosetta.rosetta.utility.sql_database.DatabaseSessionManager static method) get_int() (in module pyrosetta.rosetta.utility.json_spirit) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_string_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t method) get_int64() (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_string_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t method) get_int_or_zero() (in module pyrosetta.rosetta.utility.json_spirit) get_integer_option() (in module pyrosetta.rosetta.basic.options) get_integer_vector_option() (in module pyrosetta.rosetta.basic.options) get_inter_atr() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_inter_rep() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_interface_delta_hbond_unsat() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_interface_delta_sasa() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_interface_deltas() (in module pyrosetta.rosetta.protocols.ligand_docking) get_interface_dG() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_interface_distance() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) get_interface_moves() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) get_interface_packing_distance() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) get_interface_packstat() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_interface_residues() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) get_interface_set() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_interfaces() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_InterfaceSasaDefinition() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) get_interpolated_esp_energy() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) get_interpolated_esp_energy_with_type() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) get_interpolator() (pyrosetta.rosetta.numeric.interpolation.spline.SplineGenerator method) get_intra_atr() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_intra_rep() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_intra_segment_requirement() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory method) get_intracomponent_and_interneighbor_resis() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_and_interneighbor_subpose() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_and_interneighbor_subs() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_and_intraneighbor_resis() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_and_intraneighbor_subpose() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_and_intraneighbor_subs() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_and_neighbor_resis() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_and_neighbor_subpose() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_and_neighbor_subs() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_resis() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_subpose() (in module pyrosetta.rosetta.core.pose.symmetry) get_intracomponent_subs() (in module pyrosetta.rosetta.core.pose.symmetry) get_intramolecular_delete_move_elements() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) get_intrares_countpair() (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) get_inversion() (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) get_invert_downstream() (pyrosetta.rosetta.core.kinematics.Jump method) get_invert_upstream() (pyrosetta.rosetta.core.kinematics.Jump method) get_ion_data() (pyrosetta.rosetta.core.io.nmr.ParamagneticDatabaseHandler method) get_ion_data_table() (pyrosetta.rosetta.core.io.nmr.ParamagneticDatabaseHandler method) get_ion_label() (pyrosetta.rosetta.core.io.nmr.ParaIon method) get_ion_type() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) get_ionization_potential() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_irms() (pyrosetta.rosetta.protocols.rpc.JSON_RPC method) get_is_do_minimize() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_is_dump_cyclic_poses() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_is_dump_peptide_pose() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_is_dump_prepared_pose() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_is_dump_report_file() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_is_report_gzip() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_is_skip_zero_isc() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_iterations() (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.trajectory.DbTrajectoryReader method) get_iterator_for_tag() (pyrosetta.rosetta.core.io.silent.SilentFileData method) get_J() (pyrosetta.rosetta.core.io.nmr.ParaIon method) get_j() (pyrosetta.rosetta.core.scoring.packstat.Octree2D method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandFragment method) get_jacobian() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) get_jacobian_chain() (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) get_jacobian_matrices() (pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1 method) get_job_index_ending_job_node() (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJobTracker method) get_job_index_starting_job_node() (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJobTracker method) get_job_node() (pyrosetta.rosetta.protocols.jd3.JobDigraph method) get_job_node_assigned() (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJobTracker method) get_job_node_complete() (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJobTracker method) get_job_node_for_job_index() (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJobTracker method) get_jump() (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover method) get_jump_atom_id() (pyrosetta.rosetta.core.kinematics.AtomTree method) get_jump_atom_ids() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) get_jump_clones() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_jump_edges() (pyrosetta.rosetta.core.kinematics.FoldTree method) get_jump_id_from_chain() (in module pyrosetta.rosetta.core.pose) get_jump_id_from_chain_id() (in module pyrosetta.rosetta.core.pose) get_jump_ids_from_chain() (in module pyrosetta.rosetta.core.pose) get_jump_ids_from_chain_ids() (in module pyrosetta.rosetta.core.pose) get_jump_name() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) get_jump_name_to_components() (in module pyrosetta.rosetta.core.pose.symmetry) (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) get_jump_name_to_subunits() (in module pyrosetta.rosetta.core.pose.symmetry) (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) get_jump_num() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) get_jump_selector() (in module pyrosetta.rosetta.core.select.jump_selector) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) get_jump_string_to_jump_num() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_jump_that_builds_residue() (pyrosetta.rosetta.core.kinematics.FoldTree method) get_jumpid() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) get_k() (pyrosetta.rosetta.protocols.normalmode.NormalMode method) get_K() (pyrosetta.rosetta.protocols.relax.LocalRelax method) get_K_cluster_engine() (in module pyrosetta.rosetta.protocols.toolbox) get_KB_description() (pyrosetta.rosetta.core.scoring.func.SplineFunc method) get_keep_existing_networks() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_km() (in module pyrosetta.rosetta.core.scoring.electron_density) (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) get_known_atoms() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) get_L() (pyrosetta.rosetta.core.io.nmr.ParaIon method) get_L_equivalent() (in module pyrosetta.rosetta.core.chemical) get_l_equivalent() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.scoring.Ramachandran method) get_L_move() (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) get_L_prime() (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) get_label() (in module pyrosetta.rosetta.protocols.ss_prediction) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_tensor method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_tensor_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_tensor_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_tensor_Ts4 method) get_landmark_resnum() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_large_frag_size() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) get_large_frage_file() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) get_largest_chunk_size() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) get_largest_glycan_tree_layer() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_largest_glycan_tree_length() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_largest_glycan_tree_size() (in module pyrosetta.rosetta.core.conformation.carbohydrates) get_last_change() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) get_last_change_was_n_terminal() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) get_last_checkpoint() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) get_last_chimaera() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) get_last_chimaera_deleted() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) get_last_LoopResult() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) get_last_move_status() (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop 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.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder 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.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover 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.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover 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.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize 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.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.forge.components.BDR 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.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) (pyrosetta.rosetta.protocols.hydrate.Hydrate method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover 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.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM 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_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover 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.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover 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.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DsspMover method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.Mover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover 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.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot 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.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop 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.PrepackMover 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.SecretionOptimizationMover 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.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover 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.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover 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.IdealizeHelicesMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax 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.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover 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.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover 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_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover 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.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover 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.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover 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.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.star.StarAbinitio 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.SideChainCopier method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler 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.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover 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.monte_carlo.StepWiseMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) get_last_pose_descriptor_string() (pyrosetta.rosetta.core.import_pose.pose_stream.ExtendedPoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.LazySilentFilePoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.MetaPoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.PDBPoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.PoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.SilentFilePoseInputStream method) get_last_protein_residue() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) get_last_residue_id() (pyrosetta.rosetta.protocols.frag_picker.CSTalosIO method) (pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO method) get_last_score() (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandAssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorer method) get_last_status() (pyrosetta.rosetta.core.chemical.modifications.ChemistryBase method) (pyrosetta.rosetta.protocols.chemistries.Chemistry method) (pyrosetta.rosetta.protocols.chemistries.PatchChemistry method) (pyrosetta.rosetta.protocols.chemistries.WrappedBaseChemistry method) get_last_struct_id() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) get_late_factory() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_lb_function_cutoff() (pyrosetta.rosetta.numeric.interpolation.spline.CompoundInterpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.Interpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.SimpleInterpolator method) get_lb_function_intercept() (pyrosetta.rosetta.numeric.interpolation.spline.CompoundInterpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.Interpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.SimpleInterpolator method) get_lb_function_slope() (pyrosetta.rosetta.numeric.interpolation.spline.CompoundInterpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.Interpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.SimpleInterpolator method) get_lbdy() (pyrosetta.rosetta.numeric.interpolation.spline.SplineGenerator method) get_lbx() (pyrosetta.rosetta.numeric.interpolation.spline.SplineGenerator method) get_lby() (pyrosetta.rosetta.numeric.interpolation.spline.SplineGenerator method) get_leap_6dof() (in module pyrosetta.rosetta.protocols.sic_dock) get_leap_lower_stub() (in module pyrosetta.rosetta.protocols.sic_dock) get_leap_upper_stub() (in module pyrosetta.rosetta.protocols.sic_dock) get_least_common_ancertor_jump() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_least_common_ancertor_virtual() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_legrand_2way_orientation() (in module pyrosetta.rosetta.core.scoring.sasa) get_legrand_atomic_overlap() (in module pyrosetta.rosetta.core.scoring.sasa) get_legrand_orientation() (in module pyrosetta.rosetta.core.scoring.sasa) get_legrand_sasa_angles() (in module pyrosetta.rosetta.core.scoring.sasa) get_legrand_sasa_masks() (in module pyrosetta.rosetta.core.scoring.sasa) get_length() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.JCouplingIO method) (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) get_lib_chi_val() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_library_by_aa() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) get_lig_conformers() (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) get_lig_restype() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) get_ligand() (pyrosetta.rosetta.protocols.sewing.hashing.LigandBindingResPlacer method) get_ligand_areas() (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilder method) get_ligand_atom_id() (pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue method) get_ligand_atom_name() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue method) get_ligand_atom_xyz() (pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue method) get_ligand_com() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) get_ligand_contact_indices() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) get_ligand_grid_scores() (in module pyrosetta.rosetta.protocols.ligand_docking) get_ligand_id() (pyrosetta.rosetta.protocols.enzdes.BackboneSampler static method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol static method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol static method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol static method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol static method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol static method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol static method) (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) get_ligand_jump_id() (pyrosetta.rosetta.protocols.enzdes.BackboneSampler static method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol static method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol static method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol static method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol static method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol static method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol static method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_ligand_jumpid() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) get_ligand_mode() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) get_ligand_prob() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) get_ligand_requirements() (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_ligand_resids() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) get_ligand_residues() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) get_ligand_resnum() (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_ligand_resnum_string() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_ligand_resnums() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) get_ligand_RMSDs() (in module pyrosetta.rosetta.protocols.ligand_docking) get_ligand_selector() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_ligand_seqpos() (in module pyrosetta.rosetta.protocols.ligand_docking) get_ligand_tether() (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) get_ligand_torsion_constraints() (in module pyrosetta.rosetta.protocols.ligand_docking) get_ligand_travel() (in module pyrosetta.rosetta.protocols.ligand_docking) get_ligand_travel_ensemble_best() (in module pyrosetta.rosetta.protocols.ligand_docking) get_ligand_weight() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_ligandchi() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) get_ligandchis() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) get_LigandMotifLibrary_user() (in module pyrosetta.rosetta.protocols.motifs) get_ligands() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_ligchi_type() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) get_ligchi_types() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) get_light_chain_type() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_light_chain_type_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_lines_from_file_data() (in module pyrosetta.rosetta.utility.io) get_link() (pyrosetta.rosetta.protocols.moves.PyMOLMover method) get_link_record() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) get_linkage_position() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_linkage_position_of_saccharide_residue() (in module pyrosetta.rosetta.core.conformation.carbohydrates) get_linker_index_asymmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper method) get_linker_indices_symmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper method) get_list_of_custom_variants() (pyrosetta.rosetta.core.chemical.ResidueProperties method) get_list_of_custom_variants_by_reference() (pyrosetta.rosetta.core.chemical.ResidueProperties method) get_list_of_properties() (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) get_list_of_variant_enums() (pyrosetta.rosetta.core.chemical.ResidueProperties method) get_list_of_variants() (pyrosetta.rosetta.core.chemical.ResidueProperties method) get_listener() (pyrosetta.rosetta.basic.mpi.MessageListenerFactory method) get_lj_hbond_dis() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) get_lj_hbond_hdis() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) get_lj_hbond_OH_donor_dis() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) get_lk_fractional_contribution() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) get_lk_fractional_contribution_for_single_water() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) get_lkb_bridge2_fractional_1way() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) get_lkbr_fractional_contribution() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) get_lkbr_fractional_contribution_noangle() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) get_lkbridge_angle_widthscale() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) get_lkd_bridge_fractional_1way() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) get_lkd_frac_dome_dist() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) get_loaded_job_indices() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) get_local_ligands() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) get_local_min_conformers() (pyrosetta.rosetta.core.chemical.rings.RingConformerSet method) get_local_print_channel_name() (pyrosetta.rosetta.basic.MemTracer method) (pyrosetta.rosetta.basic.MemTracerImpl method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerImpl method) get_local_sequence_mapping() (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) get_localstrandpair_penalty() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) get_logger() (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) get_logL_values() (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_Potential method) get_loop() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) get_loop_angle_conf() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) get_loop_atom() (in module pyrosetta.rosetta.core.scoring.loop_graph) get_loop_close_potential() (in module pyrosetta.rosetta.core.scoring.loop_graph) get_loop_combine_rate() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) get_loop_file() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_loop_file_reader() (pyrosetta.rosetta.protocols.loops.Loops static method) get_loop_info() (in module pyrosetta.rosetta.protocols.mpi_refinement) get_loop_info_full() (in module pyrosetta.rosetta.protocols.mpi_refinement) get_loop_rmsd() (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) get_loop_sequence() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) get_loop_size() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_LoopCloseSixDPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_loops() (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) get_lower_bound_dy() (pyrosetta.rosetta.core.scoring.func.SplineFunc method) get_lower_bound_x() (pyrosetta.rosetta.core.scoring.func.SplineFunc method) get_lower_bound_y() (pyrosetta.rosetta.core.scoring.func.SplineFunc method) get_lower_cutpoint_partner_for_upper() (in module pyrosetta.rosetta.core.scoring.methods) get_lower_fasta() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) get_lower_pose() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) get_lowest_energy_conformer() (pyrosetta.rosetta.core.chemical.rings.RingConformerSet method) get_lowest_score() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_lowres_scorefxn() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) get_LW_orientation() (in module pyrosetta.rosetta.core.pose.rna) get_LW_orientation_from_char() (in module pyrosetta.rosetta.core.chemical.rna) get_LW_orientation_from_num() (in module pyrosetta.rosetta.core.chemical.rna) get_main_group() (pyrosetta.rosetta.core.chemical.Element method) get_mainchain_child() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_mainchain_children() (in module pyrosetta.rosetta.core.pose.carbohydrates) get_mainchain_torsions_covered() (pyrosetta.rosetta.core.chemical.mainchain_potential.MainchainScoreTable method) (pyrosetta.rosetta.core.scoring.RamaPrePro method) get_mainchain_torsions_from_coords() (pyrosetta.rosetta.core.chemical.mainchain_potential.MainchainScoreTable method) get_manager() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager static method) get_map() (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap method) get_mapfile() (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) get_mapping() (pyrosetta.rosetta.core.chemical.modifications.ChemistryBase method) (pyrosetta.rosetta.protocols.chemistries.Chemistry method) (pyrosetta.rosetta.protocols.chemistries.PatchChemistry method) (pyrosetta.rosetta.protocols.chemistries.WrappedBaseChemistry method) get_mArray() (in module pyrosetta.rosetta.utility.json_spirit) get_masks() (in module pyrosetta.rosetta.core.scoring) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) get_master_subunit_selection() (in module pyrosetta.rosetta.core.select) get_matching_fragments() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) get_matching_landmark() (in module pyrosetta.rosetta.protocols.antibody) get_matching_motifs() (pyrosetta.rosetta.core.scoring.motif.MotifHash method) (pyrosetta.rosetta.core.scoring.motif.MotifHashManager method) get_mathmatrix() (pyrosetta.rosetta.numeric.MathNTensor_double_1_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_2_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_4_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_5_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_6_t method) get_matrix_A() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) get_max0() (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) get_max_angle_dev() (pyrosetta.rosetta.protocols.membrane.FlipMover method) get_max_attempts() (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) get_max_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) get_max_centroid_to_atom_distance() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body) get_max_chainbreak() (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) get_max_cycles() (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_max_dist_ndx() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) get_max_distance() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) get_max_dslf_energy() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) get_max_dslf_pot() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) get_max_ensemble_size() (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel method) get_max_iter() (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) get_max_kic_build_attempts() (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC method) get_max_mutations() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) get_max_networks_size() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_max_nstruct() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) get_max_num_segments() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_max_omega() (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) get_max_packet_size() (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) get_max_pbond() (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) get_max_rama() (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) get_max_rms() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) get_max_segment_length() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_max_segments() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementSet method) get_max_sheet_id() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_max_strand_dist_cutoff() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) get_max_temp_for_current_round() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_SigmoidalTemperatureScheduleGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator method) get_max_unsat() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_max_value() (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid method) get_maxE_contribution_to_pi_system() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_maximum_clashes_allowed() (pyrosetta.rosetta.protocols.sewing.requirements.ClashRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandClashRequirement method) get_maximum_length() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.SegmentEnvelope method) (pyrosetta.rosetta.protocols.sewing.requirements.DsspSpecificLengthRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LengthInResiduesRequirement method) get_maximum_scores() (in module pyrosetta.rosetta.core.sequence) get_maximum_size() (pyrosetta.rosetta.protocols.sewing.requirements.SizeInSegmentsRequirement method) get_maximum_unpenalized_variance() (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) get_maxiterminimize() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) get_maxRad() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) get_mc() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.LoopRebuild method) get_MC() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) get_mc() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) get_mc_kt() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) get_mc_temperature() (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) get_mean_sugar_pucker_dependent_chi() (pyrosetta.rosetta.core.scoring.dna.DNA_DihedralPotential method) get_median_rms() (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) get_mem_foot_print() (pyrosetta.rosetta.protocols.loophash.BackboneDB method) (pyrosetta.rosetta.protocols.loophash.BackboneSegment method) get_membrane_depth_dependent_weight() (in module pyrosetta.rosetta.core.scoring.hbonds) get_Membrane_FAPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_MembraneData() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_MembranePotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_menv_params_for_residue() (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) get_message() (pyrosetta.rosetta.core.pack.task.ResfileReaderException method) get_metal_binding_atoms() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.conformation.Residue method) get_metal_center() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) get_metal_coord_bounds() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) get_metal_ion_label() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) get_metal_resnums_string() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) get_metal_selector() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) get_metals_angle_constraint_multiplier() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) get_metals_detection_LJ_multiplier() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) get_metals_distance_constraint_multiplier() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) get_metric_from_datamap_and_subtags() (in module pyrosetta.rosetta.core.simple_metrics) get_metric_names() (in module pyrosetta.rosetta.core.chemical.rdkit) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric method) (pyrosetta.rosetta.protocols.filters.FilterValueMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric method) get_metrics_from_datamap_and_subtags() (in module pyrosetta.rosetta.core.simple_metrics) get_mg_ligands() (in module pyrosetta.rosetta.protocols.magnesium) get_mg_positions() (pyrosetta.rosetta.protocols.magnesium.SampleGrid method) get_mg_potential_costheta_gaussian_parameter() (pyrosetta.rosetta.core.scoring.magnesium.MgKnowledgeBasedPotential method) get_mg_potential_costheta_indirect_gaussian_parameter() (pyrosetta.rosetta.core.scoring.magnesium.MgKnowledgeBasedPotential method) get_mg_potential_gaussian_parameter() (pyrosetta.rosetta.core.scoring.magnesium.MgKnowledgeBasedPotential method) get_mg_potential_indirect_gaussian_parameter() (pyrosetta.rosetta.core.scoring.magnesium.MgKnowledgeBasedPotential method) get_mg_res() (in module pyrosetta.rosetta.protocols.magnesium) get_mg_rsd() (in module pyrosetta.rosetta.protocols.magnesium) get_mg_scorefxn() (in module pyrosetta.rosetta.protocols.magnesium) get_mg_water_pairs() (in module pyrosetta.rosetta.protocols.magnesium) get_mhc_csv_contents() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_mhc_map_from_db() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_mhc_matrix_contents() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_middle_residue() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) get_middle_ss() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) get_midpoint_longest_loop() (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) get_min0() (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) get_min_allowed_score() (pyrosetta.rosetta.protocols.frag_picker.scores.ABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) get_min_bb() (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) get_min_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) get_min_cent_dist() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_min_chi() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_min_cst() (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) get_min_cycles() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_min_dist() (pyrosetta.rosetta.protocols.splice.RotLibOut method) get_min_distance() (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_min_eps() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_min_lig() (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) get_min_networks_size() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_min_omg() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_min_options() (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) get_min_rb() (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) get_min_rms() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) get_min_sc() (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) get_min_scorefunction() (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) get_min_sfxn() (pyrosetta.rosetta.protocols.relax.LocalRelax method) get_min_temp_for_current_round() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_SigmoidalTemperatureScheduleGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator method) get_min_type() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) get_min_value() (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid method) get_minimization_mode_enum_from_string() (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover static method) get_minimization_mode_string_from_enum() (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover static method) get_minimization_node() (pyrosetta.rosetta.core.scoring.MinimizationGraph method) get_minimize_best_tensor() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 method) get_minimize_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_minimize_with_cst() (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) get_minimizer() (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) get_minimum_length() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.SegmentEnvelope method) (pyrosetta.rosetta.protocols.sewing.requirements.DsspSpecificLengthRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LengthInResiduesRequirement method) get_minimum_size() (pyrosetta.rosetta.protocols.sewing.requirements.SizeInSegmentsRequirement method) get_minval_binwidth() (in module pyrosetta.rosetta.core.scoring.loop_graph.evaluator) get_mirror_z() (pyrosetta.rosetta.core.conformation.symmetry.VirtualCoordinate method) get_mirrored_type() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_missing_template_other_res() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) get_missing_template_res() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) get_MMBondAngleLibrary() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_MMBondLengthLibrary() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_MMLJEnergyTable() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_MMLJLibrary() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_MMTorsionLibrary() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_mObject() (in module pyrosetta.rosetta.utility.json_spirit) get_mode() (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) get_mode_as_string() (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) get_mode_i() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams method) get_model_file_name() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_model_node() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) get_model_segments() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) get_modeler_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) get_modifiable_terminus() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_module_names_from_xsd() (in module pyrosetta.rosetta.utility.xsd_util) get_module_type_as_it_appears_in_xsd() (in module pyrosetta.rosetta.utility.xsd_util) get_mono_aa_pose_copy() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) get_most_recent_total_score() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) get_motif_atom_mask() (in module pyrosetta.rosetta.core.scoring.motif) get_motif_build_position_defs_user() (in module pyrosetta.rosetta.protocols.motifs) get_motif_build_positions_user() (in module pyrosetta.rosetta.protocols.motifs) get_motif_fragments_RMSD() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch method) get_motif_hash_BB_BB() (pyrosetta.rosetta.core.scoring.motif.MotifHashManager method) get_motif_hash_BB_PH() (pyrosetta.rosetta.core.scoring.motif.MotifHashManager method) get_motif_hash_BB_PO() (pyrosetta.rosetta.core.scoring.motif.MotifHashManager method) get_motif_hash_by_fname() (pyrosetta.rosetta.core.scoring.motif.MotifHashManager method) get_motif_hash_SC_BB() (pyrosetta.rosetta.core.scoring.motif.MotifHashManager method) get_motif_hash_SC_SC() (pyrosetta.rosetta.core.scoring.motif.MotifHashManager method) get_motif_length() (in module pyrosetta.rosetta.core.sequence) get_motif_ranges() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch method) get_motif_summary() (pyrosetta.rosetta.core.scoring.motif.MotifHash method) get_MotifLibrary_user() (in module pyrosetta.rosetta.protocols.motifs) get_motifs() (pyrosetta.rosetta.core.scoring.rna.RNA_Motifs method) get_movable_jumps() (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) get_move_elements_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) get_move_elements_from_full_model_info_const() (in module pyrosetta.rosetta.core.pose.full_model_info) get_move_positions() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) get_move_type() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) get_move_type_string() (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo) get_moveable_dofs() (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) get_movemap() (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) get_movemap_factory() (in module pyrosetta.rosetta.core.select.movemap) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) get_MoveMap_for_AllCDRsSideChains_and_H3backbone() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_MoveMap_for_Loops() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_MoveMap_for_LoopsandDock() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_movemap_from_task() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) get_movement() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) get_mover() (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.wum.MoverList method) get_mover_cycles() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) get_mover_names_from_xsd() (in module pyrosetta.rosetta.utility.xsd_util) get_movers() (pyrosetta.rosetta.protocols.moves.CompositionMover method) get_moving_res() (in module pyrosetta.rosetta.protocols.rna.denovo) get_moving_res_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) get_moving_res_from_full_model_info_const() (in module pyrosetta.rosetta.core.pose.full_model_info) get_moving_res_including_domain_boundaries() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_multi_native() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) get_multi_native_com() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) get_multi_native_mca() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) get_multi_residue_ligand_RMSDs() (in module pyrosetta.rosetta.protocols.ligand_docking) get_multi_water_fade() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) get_multichain_constructor() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_MultipoleElecPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_mutant_averaged_score_components() (pyrosetta.rosetta.protocols.ddg.ddGMover method) get_mutant_averaged_totals() (pyrosetta.rosetta.protocols.ddg.ddGMover method) get_mutant_min_score_components() (pyrosetta.rosetta.protocols.ddg.ddGMover method) get_mutant_min_totals() (pyrosetta.rosetta.protocols.ddg.ddGMover method) get_mutate_label() (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) get_mutation_pairs() (pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet method) get_mutations() (pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet method) get_n() (pyrosetta.rosetta.core.energy_methods.FAElecContextData method) get_N1_lonepair_donor_angle() (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_Potential method) get_n_alignments() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) get_n_baserotamers_for_rotblock() (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet method) get_n_bb() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_N_C_stems_foldtree() (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) get_n_candidates() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) get_n_centroids() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_n_chi() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_n_co_substrates() (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) get_n_cyd_seqpos() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) get_n_frags() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) get_n_glycosidic_torsions_in_res() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_n_lanthanides() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_Ts4 method) get_n_most_segment() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment static method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment static method) get_n_multi_data() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManager method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManagerSingleton method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameterManager method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameterManager method) get_n_orientational_templates() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD method) get_n_partners() (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) get_n_pcs() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_per_lanthanides method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_per_lanthanides_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_per_lanthanides_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_per_lanthanides_Ts4 method) get_n_reactive_sites() (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) get_n_repeats() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) get_n_residue_groups() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) get_n_residue_types() (pyrosetta.rosetta.core.conformation.RotamerSetBase method) (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) get_n_rigid_body_rounds() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) get_n_rotamers_for_residue_group() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) get_n_rotamers_for_residue_type() (pyrosetta.rosetta.core.conformation.RotamerSetBase method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) get_n_sampling_rotamers_for_rotblock() (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet method) get_n_tail_res() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) get_N_term_DSSP() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) get_N_term_length() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) get_n_terminal_neighbor() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) get_n_terminal_parent() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) get_n_terminal_segment() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) get_n_torsion_rounds() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) get_n_trial_min() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter method) get_NACCESS_SASA_radii() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData method) get_NACCESS_SASA_radii_with_expanded_polars() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData method) get_name() (in module pyrosetta.rosetta.core.chemical.rdkit) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AROMATIC method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.CHARGED method) (pyrosetta.rosetta.core.pack.task.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.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PROPERTY method) (pyrosetta.rosetta.core.pack.task.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType static method) (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel method) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.ExclusivelySharedJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpForResidue method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelector method) (pyrosetta.rosetta.core.select.residue_selector.BFactorSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BlockSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ChainSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ConfluentSelector method) (pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.FractionSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelector method) (pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector method) (pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelector method) (pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelector method) (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop 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.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.ResnumFromStringsWithRangesSelector method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder 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.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) (pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter 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.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover 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.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.claims.EnvLabelSelector method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize 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.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ConstraintResidueSelector method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.CutpointResidueSelector method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ProteinResidueSelector method) (pyrosetta.rosetta.protocols.forge.components.BDR 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.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelector method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) (pyrosetta.rosetta.protocols.hydrate.Hydrate method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.OmegaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover 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.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM 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_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover 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.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover 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.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DsspMover method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.Mover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.pockets.SmallMol method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover 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.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot 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.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop 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.PrepackMover 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.SecretionOptimizationMover 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.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover 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.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.qsarPoint method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.AllAtomNormalization method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChiAngleNormalization method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HeavyAtomNormalization method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.MolecularWeightNormalization method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoreNormalization method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover 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.IdealizeHelicesMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) (pyrosetta.rosetta.protocols.residue_selectors.HBondSelector method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.NativeSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover 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.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover 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_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporter method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelector method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerChiDiff method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerElecDensDiff method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerRotBins method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolMinPack method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolPackRotamers method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolReferenceStructure method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRelax method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRotamerTrials method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRTMin method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.requirements.AssemblyRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.ClashRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.DsspSpecificLengthRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.KeepLigandContactsRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LengthInResiduesRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandAssemblyRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandClashRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.NonTerminalStartingSegmentRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.SizeInSegmentsRequirement method) (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandAssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorer method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover 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.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler2D method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler3D method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerND method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover 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.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover 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.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.star.StarAbinitio 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.SideChainCopier method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler 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.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover 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.monte_carlo.StepWiseMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) (pyrosetta.rosetta.utility.json_spirit.Config_map_std_basic_string_wchar_t_t static method) (pyrosetta.rosetta.utility.json_spirit.Config_map_std_string_t static method) (pyrosetta.rosetta.utility.json_spirit.Config_vector_std_string_t static method) get_name1_name3() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapDatabase method) get_name_individual_mover() (pyrosetta.rosetta.protocols.moves.RandomMover method) get_name_of_last_sampler_used() (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) get_native() (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) get_native_pose() (in module pyrosetta.rosetta.protocols.constraint_generator) (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop 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.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder 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.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover 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.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover 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.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize 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.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.forge.components.BDR 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.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) (pyrosetta.rosetta.protocols.hydrate.Hydrate method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobResult method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover 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.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM 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_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover 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.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover 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.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DsspMover method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.Mover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover 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.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot 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.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop 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.PrepackMover 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.SecretionOptimizationMover 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.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover 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.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover 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.IdealizeHelicesMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax 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.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover 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.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover 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_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover 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.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover 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.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover 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.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.star.StarAbinitio 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.SideChainCopier method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler 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.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover 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.monte_carlo.StepWiseMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) get_native_sequence() (in module pyrosetta.rosetta.protocols.antibody.design) get_native_sequence_matching_current_length() (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) get_native_topology() (pyrosetta.rosetta.protocols.abinitio.PairingStatistics method) get_native_vec() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_natom() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) get_natoms() (pyrosetta.rosetta.core.scoring.PQR method) get_nbr() (pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler method) get_nbr_atom_centroid() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_nbr_atom_non_ellipsoid_centroid() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_nbrhood_bfacs() (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) get_nbrs() (in module pyrosetta.rosetta.core.scoring.motif) get_Ncap_scores() (pyrosetta.rosetta.protocols.helix_capper.HelixNCapperMover method) get_ncyc() (pyrosetta.rosetta.protocols.relax.LocalRelax method) get_ndata() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) get_ndx_list() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) get_near_interface_residues() (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) get_nearest_neighbour_esp_energy() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) get_nearest_res_from_strand() (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) get_nearest_residue() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStub method) get_nearest_stub() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) get_negative_filters() (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter method) get_neighbor_atom() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential method) get_neighbor_distance() (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) get_neighbor_graph() (pyrosetta.rosetta.protocols.relax.LocalRelax method) get_neighbor_list() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) get_neighbor_residues() (in module pyrosetta.rosetta.core.select) get_neighbor_resis() (in module pyrosetta.rosetta.core.pose.symmetry) get_neighbor_subpose() (in module pyrosetta.rosetta.core.pose.symmetry) get_neighbor_subs() (in module pyrosetta.rosetta.core.pose.symmetry) get_neighborcount() (pyrosetta.rosetta.protocols.simple_moves.AtomHash method) get_neighbors() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) get_net_charge() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) get_net_sim() (pyrosetta.rosetta.protocols.cluster.APCluster method) get_net_vec() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_network_by_id() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_networks() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_new_job_id() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.BOINCJobDistributor method) (pyrosetta.rosetta.protocols.jd2.FileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.ShuffleFileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.VectorPoseJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor method) get_new_JobInputter() (pyrosetta.rosetta.protocols.jd2.JobInputterFactory method) get_new_JobOutputter() (pyrosetta.rosetta.protocols.jd2.JobOutputterFactory method) get_nexp() (pyrosetta.rosetta.protocols.relax.LocalRelax method) get_next_filenames() (pyrosetta.rosetta.protocols.ddG.ddGData method) get_next_local_jobid() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.EvenlyPartitionedNodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) get_next_nonredundant_motifmatch() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) get_next_output() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) get_next_reference_node() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) get_next_solutions() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) get_next_starting_res_for_connecting_strands() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_njumps_subunit() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) get_nmer_pssm() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_nmer_svm() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_nmer_svm_aa_matrix() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_nmer_svm_list_file_contents() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_nmer_svm_rank() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_nmer_svm_rank_list_file_contents() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_nmoves() (pyrosetta.rosetta.protocols.moves.RepeatMover method) get_nmr_data() (pyrosetta.rosetta.core.scoring.nmr.NMRDataFactory method) get_no_design_cys() (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) get_no_frags() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_nobs() (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer method) get_node() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintGraph method) (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.jd3.JobDigraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t method) (pyrosetta.rosetta.utility.graph.LowMemGraphBase method) get_node_index() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NodeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.utility.graph.DirectedNode method) (pyrosetta.rosetta.utility.graph.LowMemNode method) (pyrosetta.rosetta.utility.graph.Node method) get_node_indices_from_model_id() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) get_node_label() (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) get_node_option() (in module pyrosetta.rosetta.utility.xsd_util) get_nodes_from_same_flexseg() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) get_non_bb_clashing_rotamers() (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) get_non_ligand_requirements() (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_non_NU_TorsionID_from_AtomIDs() (in module pyrosetta.rosetta.core.conformation.carbohydrates) get_nonconst_current_contacts() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) get_nonconst_instance() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters static method) get_nonconst_ligand_contact_indices() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) get_nonconst_ligand_residues() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) get_nonconst_ligands() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_nonconst_owner_segment() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) get_nonideal() (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRelax method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRTMin method) get_nonjump_atom() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) get_nonpivot_torsion_sampling() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) get_nonzero_weighted_scoretypes() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) get_norepack1() (pyrosetta.rosetta.protocols.docking.DockTaskFactory method) get_norepack2() (pyrosetta.rosetta.protocols.docking.DockTaskFactory method) get_normal() (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method)

get_normal_to_plane() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_normalization_factor() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_per_lanthanides method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_per_lanthanides_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_per_lanthanides_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_per_lanthanides_Ts4 method) get_normalization_factor_inversed() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide method) get_normalization_type() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) get_npdhb_deltaE_for_substitution() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) get_npdhb_simple_node() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) get_nps() (pyrosetta.rosetta.protocols.constel.ChainTerm method) get_nr_class() (pyrosetta.rosetta.utility.libsvm.Svm_rosetta method) get_nr_frags() (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) get_nres_asu() (in module pyrosetta.rosetta.protocols.cryst) get_nres_asymmetric_unit() (in module pyrosetta.rosetta.core.pose.symmetry) get_nres_subunit() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) get_nrot_dofs() (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) get_nrounds() (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) get_Nstem_foldtree() (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) get_nsubdivisions() (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) get_nterm_insert_flexibility() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) get_nterm_scaffold_flexibility() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) get_nterminal_peptide_bond_reference_frame() (in module pyrosetta.rosetta.core.pose.motif) get_nterminal_peptide_bond_reference_frame_atomids() (in module pyrosetta.rosetta.core.pose.motif) get_nth_element() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManagerStorageMatrix method) get_nth_job_result_id() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.EvenlyPartitionedNodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) get_ntrials() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) get_ntries_before_giving_up() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) get_nu() (pyrosetta.rosetta.core.kinematics.MoveMap method) get_num_aa_types() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) get_num_aatypes() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) get_num_atoms() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) get_num_bbs() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_num_bytes() (in module pyrosetta.rosetta.core.scoring) get_num_chi() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_num_clusters() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_num_components() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) get_num_covered() (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) get_num_covered_total() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) get_num_decoys_used_in_calculations() (pyrosetta.rosetta.protocols.ddg.ddGMover method) get_num_digits() (in module pyrosetta.rosetta.utility) get_num_distinct_backbones() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) get_num_edges() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) get_num_edges_for_res() (in module pyrosetta.rosetta.protocols.hbnet) get_num_edges_to_larger_indexed_nodes() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NodeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.utility.graph.Node method) get_num_edges_to_smaller_indexed_nodes() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NodeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.utility.graph.Node method) get_num_exemplars() (pyrosetta.rosetta.protocols.cluster.APCluster method) get_num_incident_edges() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NodeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) get_num_interface_residues() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_num_iterations() (pyrosetta.rosetta.protocols.trajectory.DbTrajectoryReader method) get_num_native_rot() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_num_native_seq() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_num_nodes() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) get_num_of_distinct_sheet_id() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_num_of_sheets_that_surround_this_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_num_points() (pyrosetta.rosetta.numeric.interpolation.spline.SplineGenerator method) get_num_protein_sc_sc_hbonds() (in module pyrosetta.rosetta.protocols.hbnet) get_num_repeats() (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilter method) get_num_res_types() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) get_num_residues_nonvirt() (in module pyrosetta.rosetta.protocols.hybridization) get_num_residues_prot() (in module pyrosetta.rosetta.protocols.hybridization) get_num_restype_groups() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) get_num_rpe_calculations_count() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) get_num_sampled() (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) get_num_shells() (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector method) get_num_states() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NodeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) get_num_states_for_aa_type() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) get_num_states_for_aa_type_for_bb() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) get_num_states_for_aa_types() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) get_num_states_for_bb() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) get_num_states_for_node() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) get_num_states_for_restype_group() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) get_num_states_per_backbone_for_node() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) get_num_strands_in_this_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_num_total_states() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) get_num_uncovered() (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) get_num_unrecognized_atoms() (pyrosetta.rosetta.core.pose.PDBInfo method) get_num_unrecognized_res() (pyrosetta.rosetta.core.pose.PDBInfo method) get_num_virtual() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_number_alignment_media() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCData method) get_number_base_pairs() (in module pyrosetta.rosetta.core.pose.rna) get_number_base_stacks() (in module pyrosetta.rosetta.core.pose.rna) get_number_bonds() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_number_cols() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) get_number_dihedrals() (in module pyrosetta.rosetta.protocols.ncbb) get_number_dofs() (pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1 method) get_number_electrons_in_bonds() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_number_electrons_in_p_orbitals() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_number_elements() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) get_number_experiments() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) get_number_hybrid_bonds() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_number_hybrid_lone_pairs() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_number_hybrid_orbitals() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_number_ligands() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) get_number_metal_ions() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSMultiSet method) get_number_missing_residues_and_connections() (in module pyrosetta.rosetta.core.pose.full_model_info) get_number_native_base_pairs() (in module pyrosetta.rosetta.core.pose.rna) get_number_of_histograms() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics method) get_number_pcs() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) get_number_pcs_grids() (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid method) get_number_pi_orbitals() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_number_pre() (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingleSet method) get_number_rdc() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingleSet method) get_number_rows() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) get_number_sigma_orbitals() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_number_spinlabel_sites() (pyrosetta.rosetta.core.scoring.nmr.pre.PREData method) get_number_tags() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSData method) get_number_unhybridized_lone_pairs() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_number_unhybridized_sigma_orbitals() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_numeric_property() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) get_NVLookupTable() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_obj() (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_string_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t method) get_occupancy_densities() (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_Potential method) get_occupancy_density() (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_Potential method) get_ocd_cutoff() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD method) get_octahedral_uniform_rotation_sampler() (in module pyrosetta.rosetta.protocols.magnesium) get_oegrid_dimensions() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) get_offset() (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData method) get_offset_table_size_in_bytes() (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t method) get_offsets_for_aatypes() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) get_old_last_score() (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandAssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorer method) get_omega() (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilter method) get_omega_preference_for_residue_in_pose() (in module pyrosetta.rosetta.core.scoring.carbohydrates) get_OmegaPreferencesFunction() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_OmegaTether() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_omg() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_omg_range() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_on_the_fly_node() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) get_on_the_fly_owner() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) get_one_body_energy() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) get_one_body_energy_current_state() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) get_one_body_energy_for_node_state() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) get_one_body_energy_for_relaxed_state() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) get_one_body_score() (pyrosetta.rosetta.protocols.loop_grower.LoopComparator method) get_one_patch() (pyrosetta.rosetta.core.chemical.Metapatch method) get_one_template_pose() (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) get_OneDDistPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_only_extend_existing() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_op() (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_core_kinematics_MoveMap_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_core_pose_Pose_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_core_scoring_bin_transitions_BinTransitionCalculator_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_protocols_antibody_AntibodyInfo_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_protocols_loops_Loops_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_chemical_AtomProperties_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_chemical_ResidueProperties_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_chemical_rotamers_RotamerLibrarySpecification_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_kinematics_MoveMap_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_pose_Pose_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_scoring_ScoreFunction_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_interpolation_spline_BicubicSpline_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_interpolation_spline_CubicSpline_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_interpolation_spline_PolycubicSplineBase_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_MathNTensorBase_double_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_protocols_loops_Loops_t method) get_op2_op1_sign() (in module pyrosetta.rosetta.core.pose.rna) get_open_mode() (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) get_optimize1() (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) get_optimize2() (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) get_optimize_cyclic_threshold() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_optimum_distance() (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) get_option_bool() (pyrosetta.rosetta.utility.tag.Tag method) get_option_int() (pyrosetta.rosetta.utility.tag.Tag method) get_option_real() (pyrosetta.rosetta.utility.tag.Tag method) get_option_size() (pyrosetta.rosetta.utility.tag.Tag method) get_option_string() (pyrosetta.rosetta.utility.tag.Tag method) get_option_type_from_name() (in module pyrosetta.rosetta.utility.xsd_util) get_options() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Sampler method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore method) (pyrosetta.rosetta.protocols.wum.DatabaseEntryWorkUnit method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.WorkUnit_Wait method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) get_options_data() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) get_optmem() (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) get_orb_H_distance_and_energy() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) get_orb_orb_E() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) get_orbital_E_neg_pos() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_orbital_enum() (pyrosetta.rosetta.core.chemical.orbitals.OrbitalTypeMapper method) get_OrbitalsLookupTable() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_orientation() (in module pyrosetta.rosetta.core.scoring) (in module pyrosetta.rosetta.core.scoring.packstat.old) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) get_orientation_from_char() (in module pyrosetta.rosetta.core.chemical.rna) get_orientation_from_num() (in module pyrosetta.rosetta.core.chemical.rna) get_orientation_template_from_db() (in module pyrosetta.rosetta.protocols.tcr) get_oriented_pose() (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) get_orig_pose() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_origin() (pyrosetta.rosetta.core.conformation.symmetry.VirtualCoordinate method) get_original_pose_rsd() (in module pyrosetta.rosetta.protocols.generalized_kinematic_closure) get_original_residue() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) get_original_residue_set() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) get_other_ind() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.TenANeighborEdge method) (pyrosetta.rosetta.core.scoring.TwelveANeighborEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) (pyrosetta.rosetta.protocols.jd3.JobDirectedEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) (pyrosetta.rosetta.utility.graph.DirectedEdge method) (pyrosetta.rosetta.utility.graph.Edge method) (pyrosetta.rosetta.utility.graph.LowMemEdge method) get_other_node() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.TenANeighborEdge method) (pyrosetta.rosetta.core.scoring.TwelveANeighborEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) (pyrosetta.rosetta.protocols.jd3.JobDirectedEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) (pyrosetta.rosetta.utility.graph.DirectedEdge method) (pyrosetta.rosetta.utility.graph.Edge method) (pyrosetta.rosetta.utility.graph.LowMemEdge method) get_other_poses() (in module pyrosetta.rosetta.core.import_pose) get_out() (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) get_out_tag() (in module pyrosetta.rosetta.protocols.vip) get_outer_cycles() (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) get_outer_radius() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) get_outeriterations() (pyrosetta.rosetta.core.pack.annealer.DebuggingAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FASTERAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbCoupledRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbLinkingRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbPwatSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.MultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.annealer.RotamerAssigningAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SequenceSymmetricAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SimAnnealerBase method) (pyrosetta.rosetta.core.pack.annealer.SmartFixbbSimAnnealer method) (pyrosetta.rosetta.protocols.flexpack.annealer.FlexbbSimAnnealer method) get_outfile_name_with_tag() (in module pyrosetta.rosetta.core.io.silent) get_outgoing_edges() (pyrosetta.rosetta.core.kinematics.FoldTree method) get_output_filename() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) get_output_frag_files() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) get_output_level() (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSQLite method) get_output_list() (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) get_output_partner() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_output_pose_count() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_output_pose_per_move() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_output_subunit() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_output_tag() (in module pyrosetta.rosetta.protocols.jobdist) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) get_output_vector() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_overhang_length() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorExternal method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorMatrix method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorSVM method) get_overlap() (in module pyrosetta.rosetta.core.scoring) (in module pyrosetta.rosetta.core.scoring.packstat.old) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) get_overlap_gap2() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) get_overlap_target_len2() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) get_overlap_width_A2() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) get_owned_ligand_residues() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) get_owner() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) get_owner_segment() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) get_P_AA() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_P_AA_ABEGO3() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_P_AA_ss() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_Paa_pp_deriv() (pyrosetta.rosetta.core.scoring.P_AA method) get_pack_input() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_pack_neighbors() (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) get_pack_sfxn() (pyrosetta.rosetta.protocols.relax.LocalRelax method) get_packer() (in module pyrosetta.rosetta.protocols.stepwise.modeler.packer) get_packer_cycles() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) get_packer_graph() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_packer_task() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_PackingAngleResidues() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_padding() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) get_pair() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) get_PairEPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_pairing() (pyrosetta.rosetta.protocols.jumping.JumpSample method) get_pairing1_() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) get_pairing2_() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) get_pairing_geometry() (in module pyrosetta.rosetta.core.scoring.dssp) (in module pyrosetta.rosetta.protocols.jumping) get_pairings_residues() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) get_pairwise_atom_energies() (in module pyrosetta.rosetta.core.scoring) get_parallel_weight() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) get_parameter() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) get_parameter_as_res_lists() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) get_parameter_hash() (in module pyrosetta.rosetta.core.scoring) get_parameters() (pyrosetta.rosetta.protocols.frag_picker.JCouplingIO method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerChiDiff method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerElecDensDiff method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerRotBins method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolMinPack method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolPackRotamers method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolReferenceStructure method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRelax method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRotamerTrials method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRTMin method) get_parametric_info() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) get_params() (pyrosetta.rosetta.core.scoring.GenTorsionParams method) (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) get_paratope_residues() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) get_parent() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.protocols.pockets.SmallMol method) get_parent_jump() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_parent_remark() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) get_parent_remark_from_line() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) get_parent_residue() (pyrosetta.rosetta.core.kinematics.FoldTree method) get_parent_virtual() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_partition_definition() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_partition_definition_by_chemical_edge() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_partition_definition_by_jump() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_partition_definition_floating_base() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) get_partner() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) get_partner_ligand() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) get_partner_ligands() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) get_partner_pdb() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_partner_residue() (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) get_partner_residue_start_stop() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_partners() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) get_patch_names() (in module pyrosetta.rosetta.core.chemical) get_patches() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_path_option() (in module pyrosetta.rosetta.basic.options) get_path_vector_option() (in module pyrosetta.rosetta.basic.options) get_pbp() (pyrosetta.rosetta.core.energy_methods.PBLifetimeCache method) get_pcs_calc() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingle method) get_pcs_data() (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) get_PCS_data_all() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManager method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManagerSingleton method) get_pcs_data_from_pose() (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy method) get_PCS_data_input_reference() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 method) get_PCS_data_line_all_reference() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 method) get_PCS_data_line_all_spin() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_Ts4 method) get_pcs_data_per_lanthanides_all() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_Ts4 method) get_pcs_err() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingle method) get_pcs_exp() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingle method) get_PCS_experimental() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) get_pcs_grids() (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid method) get_pcs_multiset_vec() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSData method) get_pcs_single_weights() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) get_pcs_singleset_vec() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSMultiSet method) get_PCS_tolerance() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) get_pcs_values() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) get_pcs_weight() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 method) get_PcsEnergyParameter_for() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameterManager method) get_PcsInputCenter_for() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenterManager method) get_PcsInputFile_all() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter method) get_PcsInputLine_all() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile method) get_pdb2pose_numbering_as_stdmap() (in module pyrosetta.rosetta.core.pose) get_pdb_and_cleanup() (in module pyrosetta.rosetta.core.import_pose) get_pdb_code_from_pose_tag() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) get_pdb_coords() (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid method) get_pdb_id() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) get_pdb_lines() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) get_pdb_names() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_pdbid method) get_pdb_numbering_from_single_string() (in module pyrosetta.rosetta.protocols.antibody.design) get_pdb_numbering_from_strings() (in module pyrosetta.rosetta.protocols.antibody.design) get_pdb_remark() (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) get_pdb_source() (pyrosetta.rosetta.protocols.features.strand_assembly.StrandFragment method) get_pdb_with_full_model_info() (in module pyrosetta.rosetta.core.import_pose) get_pddf() (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) get_pep_lengths() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_peptide() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) get_peptide_bond_reference_frame() (in module pyrosetta.rosetta.core.pose.motif) get_peptide_bond_reference_frame_atomids() (in module pyrosetta.rosetta.core.pose.motif) get_peptide_chain() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) get_peptide_length() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorExternal method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorMatrix method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorSVM method) get_per_atom_sap() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintHelper method) get_per_residue_energy() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_per_residue_probabilities_metric_data() (pyrosetta.rosetta.core.simple_metrics.SimpleMetricData method) get_per_residue_probabilities_metric_output() (pyrosetta.rosetta.core.simple_metrics.SimpleMetricData method) get_per_residue_real_metric_data() (pyrosetta.rosetta.core.simple_metrics.SimpleMetricData method) get_per_residue_real_metric_output() (pyrosetta.rosetta.core.simple_metrics.SimpleMetricData method) get_per_residue_scores() (in module pyrosetta.rosetta.protocols.relax) get_per_residue_string_metric_data() (pyrosetta.rosetta.core.simple_metrics.SimpleMetricData method) get_per_residue_string_metric_output() (pyrosetta.rosetta.core.simple_metrics.SimpleMetricData method) get_percentile_bounds() (in module pyrosetta.rosetta.numeric.kdtree) get_period() (pyrosetta.rosetta.core.chemical.Element method) get_permissible_secondary_structures() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.SegmentEnvelope method) get_permissible_segment_ends() (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) get_permissible_termini() (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) get_perturb_CCD_off() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) get_perturb_cycles() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) get_perturb_KIC_off() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) get_perturb_show() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) get_perturb_temp() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) get_perturber() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_perturber_effect() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) get_perturber_effect_from_name() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber static method) get_perturber_effect_name() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber static method) get_perturber_names() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) get_phi() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) get_phi_from_rsd() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) get_phosphate_atom_and_neighbor_list() (in module pyrosetta.rosetta.core.pose.rna) get_phosphate_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) get_pi_electron_contribution_type() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_picked_positions() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_pivot_picker() (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) get_pivot_residues() (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) get_pivot_residues_from_movemap() (in module pyrosetta.rosetta.protocols.backrub) get_pleating() (in module pyrosetta.rosetta.core.scoring.dssp) (in module pyrosetta.rosetta.protocols.jumping) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) get_pocket_distance() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) get_point() (pyrosetta.rosetta.protocols.qsar.qsarMap method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid method) get_points() (pyrosetta.rosetta.numeric.interpolation.spline.SplineGenerator method) get_points_to_search() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) get_PointWaterPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_PoissonBoltzmannPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_polarization_from_fields() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) get_PolycubicSpline_F() (in module pyrosetta.rosetta.numeric.interpolation.spline) get_PolycubicSpline_gradient() (in module pyrosetta.rosetta.numeric.interpolation.spline) get_polymer_residue_direction() (pyrosetta.rosetta.core.kinematics.FoldTree method) get_polymer_type() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) get_pool() (pyrosetta.rosetta.cppdb.backend.connection method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) get_pool_bins() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) get_pool_name() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) get_port() (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) get_pose() (pyrosetta.rosetta.core.energy_methods.PBLifetimeCache method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.InnerMultiThreadingJob method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) (pyrosetta.rosetta.protocols.trajectory.DbTrajectoryReader method) (pyrosetta.rosetta.protocols.wum.SilentStructStore method) get_pose_build_resids() (pyrosetta.rosetta.protocols.match.Matcher method) get_pose_chains() (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) get_pose_cis_trans_conformation() (in module pyrosetta.rosetta.protocols.antibody.clusters) get_pose_data() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) get_pose_from_claimer() (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) get_pose_intensities() (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) get_pose_list() (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) get_pose_pack_data() (pyrosetta.rosetta.core.scoring.packstat.SimplePDB method) get_pose_resnum() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) get_pose_segment_dssp() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_pose_segment_ends_string() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_pose_segment_starts_string() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_pose_vector() (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) get_poses() (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.trajectory.DbTrajectoryReader method) get_position() (pyrosetta.rosetta.protocols.topology_broker.claims.CutClaim method) get_positive_filters() (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter method) get_possible_base_residue_types() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) get_possible_base_unpatchable_residue_types() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) get_possible_coordinations() (pyrosetta.rosetta.protocols.sewing.hashing.LigandBindingResPlacer method) get_possible_O3prime_C5prime_distance_range() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) get_possible_reference_res_list_from_pose_without_fold_tree() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) get_possible_unpatchable_residue_types() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) get_potential() (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondPotential method) (pyrosetta.rosetta.core.scoring.PoissonBoltzmannPotential method) get_potential_RNA() (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondPotential method) get_potential_vect() (pyrosetta.rosetta.core.scoring.func.SplineFunc method) get_potential_vect_size() (pyrosetta.rosetta.core.scoring.func.SplineFunc method) get_potentials() (pyrosetta.rosetta.core.scoring.interface_.DDPlookup method) (pyrosetta.rosetta.core.scoring.nv.NVlookup method) get_pq_schema() (pyrosetta.rosetta.utility.sql_database.session method) get_pr_idx() (pyrosetta.rosetta.core.scoring.packstat.MultiProbePerSphereAccumulator method) (pyrosetta.rosetta.core.scoring.packstat.MultiProbePoseAccumulator method) get_pre_calc() (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingle method) get_pre_data() (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) get_pre_data_file() (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) get_pre_data_from_pose() (pyrosetta.rosetta.protocols.nmr.pre.PREEnergy method) get_pre_err() (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingle method) get_pre_exp() (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingle method) get_pre_ligand_atom_id() (pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue method) get_pre_multiset_vec() (pyrosetta.rosetta.core.scoring.nmr.pre.PREData method) get_pre_pre_ligand_atom_id() (pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue method) get_pre_rate_type() (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingleSet method) get_pre_single_vec() (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingleSet method) get_pre_single_weights() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) get_pre_singleset_vec() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) get_pre_spin_type() (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingle method) get_pre_values() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) get_prediction_name() (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) get_predictor() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup method) get_prefix() (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) get_preliminary_job_node_indices() (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJobTracker method) get_prepack_only() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) get_prepared_statement() (pyrosetta.rosetta.cppdb.backend.connection method) get_prepared_uncached_statement() (pyrosetta.rosetta.cppdb.backend.connection method) get_pretend_phi_explicit() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) get_pretend_psi_explicit() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) get_primary_graft_mover() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) get_principal_quantum_number() (pyrosetta.rosetta.core.chemical.ElectronConfiguration static method) get_priority() (pyrosetta.rosetta.protocols.frag_picker.scores.ABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) get_prob() (in module pyrosetta.rosetta.protocols.ss_prediction) get_probability() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_probability_for_rotamer() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) get_probe_scorefxn() (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_Potential method) get_probe_xyz() (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_Potential method) get_profile() (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.splice.SpliceSegment method) get_profile_wgt() (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) get_proline_correction_for_node() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) get_prolines() (pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet method) get_property() (pyrosetta.rosetta.core.chemical.Element method) get_property_effect_name() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) get_property_from_name() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) get_property_from_string() (pyrosetta.rosetta.core.chemical.ResidueProperties static method) get_property_name() (pyrosetta.rosetta.core.chemical.Element static method) get_proposed_energy() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge method) get_ProQPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_protein() (pyrosetta.rosetta.protocols.loophash.BackboneDB method) get_protein_chis() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) get_protein_mass() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) get_protein_restype() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) get_protein_spins() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingle method) (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingle method) get_protein_sstype() (pyrosetta.rosetta.protocols.simple_filters.AbinitioBaseFilter method) (pyrosetta.rosetta.protocols.simple_filters.COFilter method) (pyrosetta.rosetta.protocols.simple_filters.RGFilter method) (pyrosetta.rosetta.protocols.simple_filters.SheetFilter method) get_protocol_and_batch_id() (in module pyrosetta.rosetta.protocols.features) get_protocol_id() (pyrosetta.rosetta.protocols.features.ProteinSilentReport method) get_proxy_by_priority() (pyrosetta.rosetta.basic.MemTracerImpl method) (pyrosetta.rosetta.basic.TracerImpl method) get_prs() (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERChiSqMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceDistribution method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJaccardMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJSMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERMiscMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEEROverlapMethod method) get_pseudobonds_to_residue() (pyrosetta.rosetta.core.conformation.Residue method) get_psi() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) get_psi_from_rsd() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) get_ptask() (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) get_ptr() (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.DataCache_basic_datacache_CacheableData_t method) (pyrosetta.rosetta.basic.datacache.DataCache_CacheableData method) (pyrosetta.rosetta.basic.datacache.DataCache_core_pose_datacache_CacheableObserver_t method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) get_pymol_chain() (in module pyrosetta.rosetta.basic) get_pymol_chain_index_1() (in module pyrosetta.rosetta.basic) get_PyMOL_model_name() (pyrosetta.rosetta.protocols.moves.PyMOLMover method) get_pymol_mover() (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) get_pymol_num_unique_ids() (in module pyrosetta.rosetta.basic) get_pymol_observer() (in module pyrosetta.rosetta.protocols.moves) get_pymol_sel_hbond_unsat() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_pymol_sel_interface() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_pymol_sel_packing() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_pymol_selection_for_atoms() (in module pyrosetta.rosetta.core.select) get_python_string() (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) get_q() (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) get_qt_mapping() (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) get_qt_mapping_general() (in module pyrosetta.rosetta.protocols.comparative_modeling) get_query_middle_res_id() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) get_query_phi_prediction() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_query_phi_prediction_conf() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_query_psi_prediction() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_query_psi_prediction_conf() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_query_residue_depth() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_query_sa_prediction() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_query_seq() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_query_seq_string() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_query_size() (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) get_query_ss() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_query_ss_string() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_question_mark_string() (in module pyrosetta.rosetta.protocols.features) get_quota_score() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) get_R() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) get_radial_disp_diffs() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) get_radial_disps() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) get_radical_atom() (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel method) get_radical_atom_coordinates() (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel method) get_radii() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) get_radius() (in module pyrosetta.rosetta.protocols.electron_density) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.scoring.packstat.AtomRadiusMap method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) get_radius_exp() (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) get_radius_of_gyration() (in module pyrosetta.rosetta.protocols.ligand_docking) get_rama_check() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) get_rama_prepro_mainchain_torsion_potential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_rama_prepro_mainchain_torsion_potential_name() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) get_rama_prepro_map_file_name() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) get_Ramachandran() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_Ramachandran2B() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_Ramachandran2B_ptr() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_Ramachandran_ptr() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_RamaPrePro() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_ramatable_name_by_type() (pyrosetta.rosetta.core.scoring.Ramachandran method) get_ramatable_type_by_name() (pyrosetta.rosetta.core.scoring.Ramachandran method) get_ramp_fa_rep() (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) get_ramp_scorefxn() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) get_ramp_width_A2() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) get_rand_glycan_jump_res() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) get_rand_range() (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover method) get_random_angle() (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) get_random_backbone_segments() (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) get_random_base_pair_jump() (pyrosetta.rosetta.core.import_pose.libraries.RNA_JumpLibrary method) get_random_beta_sheet_jump() (pyrosetta.rosetta.protocols.jumping.PairingLibrary method) (pyrosetta.rosetta.protocols.jumping.SpecificGeometryLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) get_random_conformer() (pyrosetta.rosetta.core.chemical.rings.RingConformerSet method) get_random_local_min_conformer() (pyrosetta.rosetta.core.chemical.rings.RingConformerSet method) get_random_loop_flag() (pyrosetta.rosetta.protocols.LoopRebuild method) get_random_neighbor() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) get_random_neighbor_for_node() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) get_random_node() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) get_random_node_with_edges() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) get_random_order() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) get_random_point_on_ellipsoid() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_random_pose() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector method) get_random_segment_id() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) get_random_tmh_jump() (pyrosetta.rosetta.protocols.jumping.PairingLibrary method) (pyrosetta.rosetta.protocols.jumping.SpecificGeometryLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) get_randomization_mode_enum_from_string() (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover static method) get_randomization_mode_string_from_enum() (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover static method) get_randomize_input_sequence() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) get_randomize_resnum() (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover method) get_range() (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover method) get_raw_const_ptr() (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.DataCache_basic_datacache_CacheableData_t method) (pyrosetta.rosetta.basic.datacache.DataCache_CacheableData method) (pyrosetta.rosetta.basic.datacache.DataCache_core_pose_datacache_CacheableObserver_t method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) get_raw_ptr() (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.DataCache_basic_datacache_CacheableData_t method) (pyrosetta.rosetta.basic.datacache.DataCache_CacheableData method) (pyrosetta.rosetta.basic.datacache.DataCache_core_pose_datacache_CacheableObserver_t method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) get_rb_atr_and_rep_scores() (in module pyrosetta.rosetta.protocols.ligand_docking) get_rb_center() (pyrosetta.rosetta.core.kinematics.Jump method) get_rb_delta() (pyrosetta.rosetta.core.kinematics.Jump method) get_rb_mover() (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) get_rb_number() (in module pyrosetta.rosetta.core.id) get_rb_seq() (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) get_rb_trial() (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) get_rb_type() (in module pyrosetta.rosetta.core.id) get_rdc_calc() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingle method) get_RDC_data() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling_Rohl method) get_rdc_data_from_pose() (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergy method) get_RDC_data_type() (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling_Rohl method) get_rdc_err() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingle method) get_rdc_exp() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingle method) get_rdc_multiset_vec() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCData method) get_rdc_single_weights() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) get_rdc_singleset_vec() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) get_rdc_type() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingle method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingleSet method) get_rdc_values() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) get_rdf_function() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) get_reactive_atom() (pyrosetta.rosetta.core.enzymes.EnzymeManager static method) get_reactive_residue_consensus_sequence_position() (pyrosetta.rosetta.core.enzymes.EnzymeManager static method) get_reactive_site_atom_name() (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) get_reactive_site_sequence_position() (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) get_ready_for_sew_packing() (in module pyrosetta.rosetta.protocols.hydrate) get_real() (in module pyrosetta.rosetta.utility.json_spirit) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_string_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t method) get_Real_MathNTensor_dimension_size() (in module pyrosetta.rosetta.numeric) get_real_metric_data() (pyrosetta.rosetta.core.simple_metrics.SimpleMetricData method) get_real_option() (in module pyrosetta.rosetta.basic.options) get_real_or_zero() (in module pyrosetta.rosetta.utility.json_spirit) get_real_vector_option() (in module pyrosetta.rosetta.basic.options) get_recces_turner_sampler() (in module pyrosetta.rosetta.protocols.recces.sampler) get_recent_history_size() (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) get_recenter() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_recognized_cdr_definitions() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) get_recognized_cluster_definitions() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) get_recognized_design_protocols() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignEnumManager method) get_recognized_numbering_schemes() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) get_recover_lowest_assembly() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_recovery_threshold() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerElecDensDiff method) get_redesign_loop() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) get_ref_atom_ID() (pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobians method) get_ref_pose() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) get_ref_tags() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) get_ref_xyz() (pyrosetta.rosetta.core.pose.rna.VDW_Grid method) get_reference_atoms() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_reference_atoms_for_1st_omega() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_reference_atoms_for_2nd_omega() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_reference_atoms_for_phi() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_reference_atoms_for_psi() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_reference_energies_from_dofs() (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) get_reference_energy() (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) get_reference_ft() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) get_reference_intensities() (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) get_reference_pose() (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) get_reference_res_for_each_virtual_sugar_based_on_fold_tree() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) get_reference_res_for_each_virtual_sugar_without_fold_tree() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) get_reference_res_for_virtual_sugar_based_on_fold_tree() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) get_reference_shift() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential method) get_refine_CCD_off() (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) get_refine_cycles() (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) get_refine_KIC_off() (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) get_refine_only() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) get_refine_repack_cycles() (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) get_refine_temp() (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) get_region_end() (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) get_region_mm_bend_score() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) get_region_of_residue() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_region_start() (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) get_region_total_score() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) get_register() (pyrosetta.rosetta.core.scoring.dssp.Pairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) get_rel_hphobic_sasa_by_charge() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_relative() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup method) get_relative_additive() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup method) get_relax_script() (pyrosetta.rosetta.protocols.relax.RelaxScriptManager method) get_relaxed_state() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) get_relevant_residues() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) get_relevant_residues_mode() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeatures method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures method) (pyrosetta.rosetta.protocols.features.AtomTypesFeatures method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeatures method) (pyrosetta.rosetta.protocols.features.DdGFeatures method) (pyrosetta.rosetta.protocols.features.FeaturesReporter method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeatures method) (pyrosetta.rosetta.protocols.features.HBondFeatures method) (pyrosetta.rosetta.protocols.features.HBondParameterFeatures method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTest method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeatures method) (pyrosetta.rosetta.protocols.features.HelixCapFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.JobDataFeatures method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeatures method) (pyrosetta.rosetta.protocols.features.ModelFeatures method) (pyrosetta.rosetta.protocols.features.OrbitalsFeatures method) (pyrosetta.rosetta.protocols.features.PairFeatures method) (pyrosetta.rosetta.protocols.features.PdbDataFeatures method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeatures method) (pyrosetta.rosetta.protocols.features.PoseConformationFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeatures method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeatures method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeatures method) (pyrosetta.rosetta.protocols.features.ResidueFeatures method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeatures method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeatures method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeatures method) (pyrosetta.rosetta.protocols.features.RotamerFeatures method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeatures method) (pyrosetta.rosetta.protocols.features.RuntimeFeatures method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeatures method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeatures method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeatures method) (pyrosetta.rosetta.protocols.features.ScreeningFeatures method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeatures method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeatures method) (pyrosetta.rosetta.protocols.features.SmotifFeatures method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeatures method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) (pyrosetta.rosetta.protocols.features.StructureFeatures method) (pyrosetta.rosetta.protocols.features.StructureScoresFeatures method) (pyrosetta.rosetta.protocols.features.TaskOperationFeatures method) (pyrosetta.rosetta.protocols.features.TotalScoreFeatures method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeatures method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeatures method) (pyrosetta.rosetta.protocols.features.WaterFeatures method) get_relevant_residues_task_factory() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) get_remodel_res() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) get_remove_hydrogens() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) get_remove_pre_pose() (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) get_repack_neighborhood() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_repack_period() (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) get_repacked_poses() (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) get_report_as() (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) get_report_format() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_representative_type() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) get_representative_type_aa() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_representative_type_base_name() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_representative_type_name1() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_representative_type_name3() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_required_resnums() (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_required_selector() (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_requirement() (pyrosetta.rosetta.protocols.sewing.requirements.AssemblyRequirementFactory method) get_requirements() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_res_bfacs() (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) get_res_centers() (pyrosetta.rosetta.core.scoring.packstat.SimplePDB method) get_res_energy() (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) get_res_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) get_res_list_as_pairs() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) get_res_list_const() (in module pyrosetta.rosetta.core.pose.full_model_info) get_res_list_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) get_res_list_from_full_model_info_const() (in module pyrosetta.rosetta.core.pose.full_model_info) get_res_num_from_pdb_info() (in module pyrosetta.rosetta.core.pose.full_model_info) get_res_res_elecE() (pyrosetta.rosetta.core.scoring.GenBornPotential method) (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) get_res_res_overlap() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) get_res_res_sasa() (pyrosetta.rosetta.core.scoring.SASAPotential method) get_res_res_score() (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) get_res_res_vdw() (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) get_res_type_set() (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) get_resample_internal_local_move_elements() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) get_resample_internal_move_elements() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) get_resample_move_elements() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) get_resample_terminal_move_elements() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) get_resfile() (pyrosetta.rosetta.core.scoring.motif.MotifHits method) get_resfile_1() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_resfile_2() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_resfile_commands() (in module pyrosetta.rosetta.core.pack.task) get_resid() (in module pyrosetta.rosetta.protocols.denovo_design) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.moves.ResId method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) get_residue() (in module pyrosetta.rosetta.core.pose.full_model_info) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.FragData method) (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer method) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.legacy_sewing.Model method) (pyrosetta.rosetta.protocols.qsar.qsarMap method) (pyrosetta.rosetta.protocols.qsar.qsarPoint method) (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) get_residue_at_origin() (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) get_residue_at_origin_with_matching_type() (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) get_residue_base_state() (in module pyrosetta.rosetta.core.chemical.rna) (in module pyrosetta.rosetta.core.pose.rna) get_residue_data() (pyrosetta.rosetta.core.scoring.GenBondedExclInfo method) get_residue_depth() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) get_residue_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) get_residue_energy_by_svm() (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) get_residue_energy_by_table() (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) get_residue_energy_from_sequence() (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) get_residue_feature() (pyrosetta.rosetta.protocols.comparative_modeling.features.ResidueFeatureFactory method) get_residue_from_name() (in module pyrosetta.rosetta.core.conformation) get_residue_from_name1() (in module pyrosetta.rosetta.core.conformation) get_residue_group_begin() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) get_residue_group_index_for_rotamer() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) get_residue_hbonds() (pyrosetta.rosetta.protocols.simple_pose_metric_calculators.NumberHBondsCalculator method) get_residue_hsasa() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_residue_hsasa_bb() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_residue_hsasa_sc() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_residue_level_task_operation_names_from_xsd() (in module pyrosetta.rosetta.utility.xsd_util) get_residue_mapping_from_selectors() (in module pyrosetta.rosetta.core.select.residue_selector) get_residue_mask() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) get_residue_names_map() (pyrosetta.rosetta.protocols.chromophore.ChromophoreDataReader method) get_residue_num() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) get_residue_pair_data() (pyrosetta.rosetta.core.scoring.GenBondedExclInfo method) get_residue_pair_rt6() (in module pyrosetta.rosetta.core.scoring.motif) get_residue_pair_xform() (in module pyrosetta.rosetta.core.scoring.motif) get_residue_path_distances() (in module pyrosetta.rosetta.core.chemical) get_residue_pucker_state() (in module pyrosetta.rosetta.core.chemical.rna) (in module pyrosetta.rosetta.core.pose.rna) get_residue_residue_h2o_hbonds_1way() (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) get_residue_sasa() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_residue_sasa_bb() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_residue_sasa_sc() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_residue_selector() (in module pyrosetta.rosetta.core.select.residue_selector) (in module pyrosetta.rosetta.protocols.denovo_design) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects method) get_residue_selector_from_subset() (in module pyrosetta.rosetta.core.select) get_residue_selector_names_from_xsd() (in module pyrosetta.rosetta.utility.xsd_util) get_residue_set_from_subset() (in module pyrosetta.rosetta.core.select) get_residue_type() (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel method) get_residue_type_begin() (pyrosetta.rosetta.core.conformation.RotamerSetBase method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) get_residue_type_index_for_rotamer() (pyrosetta.rosetta.core.conformation.RotamerSetBase method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) get_residue_type_set() (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) get_residue_type_with_custom_variant_added() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_residue_type_with_variant_added() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_residue_type_with_variant_removed() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) get_residue_vector() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) get_residue_weight() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) get_residue_weight_by_ss() (in module pyrosetta.rosetta.core.scoring.methods) get_residue_weights() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) get_residues() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobians method) (pyrosetta.rosetta.protocols.ligand_docking.Ligand_info method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation method) get_residues_from_chains() (in module pyrosetta.rosetta.core.pose) get_residues_from_movemap_bb_any_torsion() (in module pyrosetta.rosetta.core.kinematics) get_residues_from_movemap_bb_or_chi() (in module pyrosetta.rosetta.core.kinematics) get_residues_from_movemap_with_id() (in module pyrosetta.rosetta.core.kinematics) get_residues_from_subset() (in module pyrosetta.rosetta.core.select) get_residues_in_rbsegment() (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) get_residues_to_preglycosylate() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) get_residues_to_rebuild() (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) get_residues_within_dist_of_RNA() (in module pyrosetta.rosetta.protocols.rna.denovo) get_resis() (in module pyrosetta.rosetta.core.pose.symmetry) get_reslabels() (pyrosetta.rosetta.core.pose.PDBInfo method) get_resname() (pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue method) get_resnum() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet method) get_resNum() (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFragment method) get_resnum() (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover method) get_resnum_and_chain() (in module pyrosetta.rosetta.utility) get_resnum_and_chain_and_segid() (in module pyrosetta.rosetta.utility) get_resnum_and_chain_from_one_tag() (in module pyrosetta.rosetta.utility) get_resnum_and_segid() (in module pyrosetta.rosetta.utility) get_resnum_and_segid_from_one_tag() (in module pyrosetta.rosetta.utility) get_resnum_from_cstid() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) get_resnum_from_cstid_list() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) get_resnum_from_glycan_position() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) get_resnum_from_pdb_numbering() (in module pyrosetta.rosetta.protocols.antibody.design) get_resnum_from_single_string() (in module pyrosetta.rosetta.protocols.antibody.design) get_resnum_from_single_string_w_landmark() (in module pyrosetta.rosetta.protocols.antibody.design) get_resnum_from_strings() (in module pyrosetta.rosetta.protocols.antibody.design) get_resnum_list() (in module pyrosetta.rosetta.core.pose) get_resnum_list_ordered() (in module pyrosetta.rosetta.core.pose) get_resnum_selector() (in module pyrosetta.rosetta.core.pose) get_resnum_string() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) get_resnum_to_subunit_component() (in module pyrosetta.rosetta.core.pose.symmetry) get_resnumber_from_reference_pose() (in module pyrosetta.rosetta.core.pose) get_resnums() (pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet method) get_resnums_for_chain() (in module pyrosetta.rosetta.core.pose) get_resnums_for_chain_id() (in module pyrosetta.rosetta.core.pose) get_resnums_from_glycan_positions() (in module pyrosetta.rosetta.core.pose.carbohydrates) get_resnums_from_strings_with_ranges() (in module pyrosetta.rosetta.protocols.antibody.design) get_resnums_in_leaf() (in module pyrosetta.rosetta.core.pose.carbohydrates) get_resnums_in_leaf_on_the_fly() (in module pyrosetta.rosetta.core.pose.carbohydrates) get_resolution_cutoff() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_resolution method) get_resolution_damping() (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) get_resrange_hbond_energy() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) get_restrict_partners_to_chains() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_restrict_receptors_to_chains() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_restype_emap() (pyrosetta.rosetta.core.scoring.SplitUnfoldedTwoBodyPotential method) get_restype_for_pose() (in module pyrosetta.rosetta.core.pose) get_result() (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) get_result_set() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results method) get_reverse_assembly() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) get_rg() (in module pyrosetta.rosetta.protocols.sic_dock) get_rh() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) get_rigid_body_confs() (pyrosetta.rosetta.protocols.hotspot_hashing.SearchPatternRotSetOp method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) get_rigid_body_jumps() (in module pyrosetta.rosetta.core.pose.rna) get_rigid_body_mover() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_rigid_body_values() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) get_ring() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) get_ring_current_deriv() (in module pyrosetta.rosetta.core.scoring.rna.chemical_shift) get_ring_params() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) get_rise() (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilter method) get_rmax() (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) get_rms() (in module pyrosetta.rosetta.protocols.electron_density) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) get_rmsd() (in module pyrosetta.rosetta.protocols.loophash) (in module pyrosetta.rosetta.protocols.stepwise.modeler.align) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) get_RMSD() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch method) get_rmsd() (pyrosetta.rosetta.protocols.pockets.SmallMol method) get_rmsd_mat() (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelEnsemble method) get_rmsd_no_superimpose() (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner method) get_RMSD_only_this() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) get_rmsd_over_all_poses() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner method) get_rmsd_stems_no_superimpose() (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) get_rmsd_target_tolerance() (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) get_rmsd_tolerance() (pyrosetta.rosetta.protocols.LoopRebuild method) get_rmsd_type_name_map() (in module pyrosetta.rosetta.core.scoring) get_rmsd_type_names() (in module pyrosetta.rosetta.core.scoring) get_RNA_AtomVDW() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_rna_base_centroid() (in module pyrosetta.rosetta.core.chemical.rna) get_rna_base_coordinate_system() (in module pyrosetta.rosetta.core.chemical.rna) get_rna_base_coordinate_system_from_CS_params() (in module pyrosetta.rosetta.core.scoring.rna.chemical_shift) get_rna_base_coordinate_system_stub() (in module pyrosetta.rosetta.core.chemical.rna) get_rna_base_pairing_status() (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential method) get_RNA_ChemicalShiftPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_RNA_CS_residue_parameters() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters method) get_rna_data_info() (in module pyrosetta.rosetta.core.io.rna) get_RNA_DMS_LowResolutionPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_RNA_DMS_Potential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_rna_hires_scorefxn() (in module pyrosetta.rosetta.protocols.rna.denovo) get_RNA_LowResolutionPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_rna_motif_score() (in module pyrosetta.rosetta.core.scoring.rna) get_rna_motifs() (in module pyrosetta.rosetta.core.scoring.rna) get_rna_secstruct_legacy() (in module pyrosetta.rosetta.core.pose.rna.secstruct_legacy) get_rna_secstruct_legacy_from_const_pose() (in module pyrosetta.rosetta.core.pose.rna.secstruct_legacy) get_rna_stack_score() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) get_rna_suite_potential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_RNAring_sasa() (pyrosetta.rosetta.protocols.pockets.GenPharmacophore method) get_rnp_docking_fold_tree() (in module pyrosetta.rosetta.protocols.rna.denovo) get_RNP_LowResPairDistPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_RNP_LowResPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_RNP_LowResStackData() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_root() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) (pyrosetta.rosetta.protocols.pockets.SmallMol method) get_root_atomno() (in module pyrosetta.rosetta.core.conformation) get_root_residue_root_atomno() (in module pyrosetta.rosetta.core.conformation) get_rosetta_restype() (pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler method) get_ROSETTA_SASA_radii() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData method) get_rosetta_thread_index() (pyrosetta.rosetta.basic.thread_manager.RosettaThreadManager method) get_rot_angle() (in module pyrosetta.rosetta.protocols.electron_density) get_rot_ind() (pyrosetta.rosetta.protocols.mean_field.ResHashMap method) get_rot_mag() (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) get_rot_magnitude() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) get_rot_step() (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) get_rotamer() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) get_rotamer_angle_diffs() (in module pyrosetta.rosetta.core.pack) get_rotamer_bounding_box() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) get_rotamer_from_chi() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) get_rotamer_recovery() (pyrosetta.rosetta.protocols.pose_metric_calculators.RotamerRecovery method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) get_rotamer_recovery_comparer() (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) get_rotamer_recovery_protocol() (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) get_rotamer_recovery_reporter() (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) get_rotamer_samples() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) get_rotamers() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) get_rotamers_born_radii() (pyrosetta.rosetta.core.scoring.facts.FACTSPotential method) (pyrosetta.rosetta.core.scoring.GenBornPotential method) get_rotamers_effective_radii() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) get_rotamers_multipole_info() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) get_rotamers_vdw_info() (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) get_rotated_and_translated_pose() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) get_rotation() (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.RT method) get_rotation_magnitude() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_rotation_matrix() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_rotation_std_dev() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover method) get_rotblock_index_for_sampling_rotamer() (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet method) get_row() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) get_rsd() (pyrosetta.rosetta.core.io.nmr.AtomSelection method) get_rsd_type_from_aa() (in module pyrosetta.rosetta.core.pose) get_rsd_type_name3() (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) get_rt_from_residue_pair() (in module pyrosetta.rosetta.core.conformation) get_rt_over_leap() (in module pyrosetta.rosetta.protocols.loophash) get_rt_over_leap_fast() (in module pyrosetta.rosetta.protocols.loophash) get_rt_over_leap_without_foldtree_bs() (in module pyrosetta.rosetta.protocols.loophash) get_run_time() (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Sampler method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore method) (pyrosetta.rosetta.protocols.wum.DatabaseEntryWorkUnit method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.WorkUnit_Wait method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) get_Rvalue() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) get_S() (pyrosetta.rosetta.core.io.nmr.ParaIon method) get_safe_max_dis2() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) get_sample_index() (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) get_sample_nonpivot_torsions() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) get_sample_res_for_pose() (in module pyrosetta.rosetta.core.pose.full_model_info) get_sampler_options() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) get_sampling_data() (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction method) get_sasa() (in module pyrosetta.rosetta.core.scoring.motif) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) get_sasa_dot_locations() (in module pyrosetta.rosetta.core.scoring.packstat) get_sasa_from_cycles() (in module pyrosetta.rosetta.core.scoring.power_diagram) get_sasa_method_from_string() (in module pyrosetta.rosetta.core.scoring.sasa) get_sasa_radii_parameter_name() (in module pyrosetta.rosetta.core.scoring.sasa) get_sasa_radii_set_from_string() (in module pyrosetta.rosetta.core.scoring.sasa) get_SASAfilter() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) get_SASAPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_sc_bb_sasa() (in module pyrosetta.rosetta.core.scoring.sasa) get_sc_bb_sasa_per_res() (in module pyrosetta.rosetta.core.scoring.sasa) get_sc_bbE() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets static method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets static method) get_sc_interface_builder() (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilder method) get_sc_min() (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) get_sc_scale() (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) get_scaffold2motif_size_change() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch method) get_scaffold_fragment_data() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch method) get_scaffold_ranges() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch method) get_scaffold_status() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStub method) get_scaling_factor() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingleSet method) get_scdepth_avrg() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) get_scdepth_fvar() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) get_scdepth_sdev() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) get_score() (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERChiSqMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERData method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDecayData method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceBounds method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceDistribution method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJaccardMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJSMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERMiscMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEEROverlapMethod method) (pyrosetta.rosetta.core.scoring.rna.TNA_SuitePotential method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreCutoffFilter method) (pyrosetta.rosetta.protocols.hbnet.HBNetScore method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyCalciumMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyInterModelMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyPartnerMotifScorer method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) (pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc method) (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreLoopsFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilter method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorer method) get_score_against_internal_contacts() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_score_best() (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) get_score_components() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) get_score_fast() (pyrosetta.rosetta.protocols.hybridization.TMalign method) get_score_for_struct_id_and_score_term_from_job_data() (in module pyrosetta.rosetta.protocols.features) get_score_for_struct_id_and_score_term_from_score_data() (in module pyrosetta.rosetta.protocols.features) get_score_function() (in module pyrosetta.rosetta.core.scoring) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.match.downstream.ScoringSecMatchRPE method) (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects method) get_score_function_attributes() (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder static method) get_score_function_legacy() (in module pyrosetta.rosetta.core.scoring) get_score_function_name() (in module pyrosetta.rosetta.core.scoring) get_score_functionName() (in module pyrosetta.rosetta.core.scoring) get_score_fxn() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_score_line_string() (in module pyrosetta.rosetta.core.pose) get_score_manager() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_score_map() (in module pyrosetta.rosetta.protocols.jobdist) get_score_multiply_subunit() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_score_name() (pyrosetta.rosetta.protocols.frag_picker.scores.ABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) get_score_normalization_function() (in module pyrosetta.rosetta.protocols.qsar.scoring_grid) get_score_offset() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup method) get_score_result() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) get_score_subunit() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_score_tolerance() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) get_score_type_id_from_score_term() (in module pyrosetta.rosetta.protocols.features) get_scored_base_stack_list() (in module pyrosetta.rosetta.core.pose.rna) get_scorefile_reporting_prefix() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_scorefilter() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) get_scorefunction() (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) get_scorefunction_header() (pyrosetta.rosetta.protocols.ddg.ddGMover method) get_scorefunction_initialized() (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) get_scorefxn() (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) (pyrosetta.rosetta.protocols.residue_selectors.HBondSelector method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) get_scorefxn_deriver() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) get_scorefxn_filename() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) get_scorefxn_info() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) get_scores() (pyrosetta.rosetta.protocols.recces.Histogram method) get_scores_map() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded method) get_scores_to_keep() (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorer method) get_scorescale() (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) get_scoretypes() (in module pyrosetta.rosetta.protocols.recces) get_scoring_scheme() (pyrosetta.rosetta.core.sequence.ScoringSchemeFactory method) get_SDE_score() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) get_second_atom() (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData method) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) get_second_atom_from_connection() (in module pyrosetta.rosetta.core.conformation) get_second_node_ind() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.TenANeighborEdge method) (pyrosetta.rosetta.core.scoring.TwelveANeighborEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) (pyrosetta.rosetta.utility.graph.Edge method) (pyrosetta.rosetta.utility.graph.LowMemEdge method) get_second_node_num_states_per_aa() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) get_second_offset() (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) get_second_substrates_or_byproducts() (pyrosetta.rosetta.core.enzymes.EnzymeManager static method) get_secondary_graft_mover() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) get_secondary_prediction() (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) get_SecondaryStructurePotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_secstruct() (in module pyrosetta.rosetta.protocols.membrane) (pyrosetta.rosetta.core.pose.rna.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) get_seed() (pyrosetta.rosetta.numeric.random.RandomGenerator method) get_seg1() (pyrosetta.rosetta.protocols.sewing.hashing.Hasher method) get_seg2() (pyrosetta.rosetta.protocols.sewing.hashing.Hasher method) get_segfile_path() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) get_segids_from_pdb_info() (in module pyrosetta.rosetta.core.pose.full_model_info) get_segment() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) get_segment_coords() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) get_segment_distance_cutoff() (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_segment_file_paths() (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) get_segment_fname() (pyrosetta.rosetta.protocols.splice.RotLibdb method) get_segment_id() (in module pyrosetta.rosetta.protocols.features.strand_assembly) (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) get_segment_names_ordered() (pyrosetta.rosetta.protocols.splice.Splice method) get_segment_vector() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_segments_from_dssp() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_select_range() (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) get_select_resnums() (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) get_selected_mover() (pyrosetta.rosetta.protocols.moves.SwitchMover method) get_selected_residues() (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionTensorflowProtocol static method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionTensorflowProtocolBase static method) get_selection_sequence() (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover static method) get_selector() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) get_selector_name() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) get_selector_type() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) get_selector_type_by_name() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) get_selector_type_name() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) get_self_ptr() (pyrosetta.rosetta.basic.datacache.CacheableData method) (pyrosetta.rosetta.basic.datacache.CacheableResRotPairFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringIntegerMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.CacheableUint64MathMatrixFloatMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.Parameter method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator method) (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.energy_methods.FAElecContextData method) (pyrosetta.rosetta.core.energy_methods.PBLifetimeCache method) (pyrosetta.rosetta.core.energy_methods.PoseSequence method) (pyrosetta.rosetta.core.energy_methods.RG_Local_MinData method) (pyrosetta.rosetta.core.energy_methods.RG_MinData method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.FragData method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphContainer method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.palette.CustomBaseTypePackerPalette method) (pyrosetta.rosetta.core.pack.palette.DefaultPackerPalette method) (pyrosetta.rosetta.core.pack.palette.NCAADefaultPackerPalette method) (pyrosetta.rosetta.core.pack.palette.NoDesignPackerPalette method) (pyrosetta.rosetta.core.pack.palette.PackerPalette method) (pyrosetta.rosetta.core.pack.rotamer_set.WaterPackingInfo method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintGraph method) (pyrosetta.rosetta.core.scoring.constraints.CstMinimizationData method) (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.DipolarCoupling method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) (pyrosetta.rosetta.core.scoring.facts.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.facts.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) (pyrosetta.rosetta.core.scoring.GenBondedExclInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.hbonds.HBond method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.MembraneTopology method) (pyrosetta.rosetta.core.scoring.methods.NeighborListData method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSData method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREData method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCData method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling_Rohl method) (pyrosetta.rosetta.core.scoring.ResidueNblistData method) (pyrosetta.rosetta.core.scoring.ResiduePairNeighborList method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.trie.TrieCollection method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricData method) (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.JumpSampleData method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.abinitio.Templates method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder 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.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover 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.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover 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.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.AutoCutData method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.Environment method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputter method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize 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.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.forge.components.BDR 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.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) (pyrosetta.rosetta.protocols.hydrate.Hydrate method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EmptyPoseJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.LazySilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.ScreeningJobInputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd3.JobDigraph method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover 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.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM 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_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.match.MatcherTask method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover 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.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover 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.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DsspMover method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.Mover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover 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.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot 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.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop 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.PrepackMover 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.SecretionOptimizationMover 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.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover 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.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputter method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover 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.IdealizeHelicesMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax 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.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover 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.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover 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_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManager method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_Ts4 method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover 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.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover 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.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover 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.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.star.StarAbinitio 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.SideChainCopier method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler 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.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover 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.monte_carlo.StepWiseMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.NCSResMapping method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.STMStoredTask method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleResidueInvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDistSasaCalculator method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.tag.Tag method) (pyrosetta.rosetta.utility.tag.XMLSchemaRepeatableCTNode method) get_self_weak_ptr() (pyrosetta.rosetta.basic.datacache.CacheableData method) (pyrosetta.rosetta.basic.datacache.CacheableResRotPairFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringIntegerMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.CacheableUint64MathMatrixFloatMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.Parameter method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator method) (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.energy_methods.FAElecContextData method) (pyrosetta.rosetta.core.energy_methods.PBLifetimeCache method) (pyrosetta.rosetta.core.energy_methods.PoseSequence method) (pyrosetta.rosetta.core.energy_methods.RG_Local_MinData method) (pyrosetta.rosetta.core.energy_methods.RG_MinData method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphContainer method) (pyrosetta.rosetta.core.pack.rotamer_set.WaterPackingInfo method) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) (pyrosetta.rosetta.core.scoring.constraints.CstMinimizationData method) (pyrosetta.rosetta.core.scoring.DipolarCoupling method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) (pyrosetta.rosetta.core.scoring.facts.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.facts.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) (pyrosetta.rosetta.core.scoring.GenBondedExclInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.MembraneTopology method) (pyrosetta.rosetta.core.scoring.methods.NeighborListData method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSData method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREData method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCData method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling_Rohl method) (pyrosetta.rosetta.core.scoring.ResidueNblistData method) (pyrosetta.rosetta.core.scoring.ResiduePairNeighborList method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) (pyrosetta.rosetta.core.scoring.trie.TrieCollection method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricData method) (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.JumpSampleData method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.abinitio.Templates method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder 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.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover 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.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover 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.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.AutoCutData method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.Environment method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputter method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize 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.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.forge.components.BDR 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.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) (pyrosetta.rosetta.protocols.hydrate.Hydrate method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EmptyPoseJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.LazySilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.ScreeningJobInputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover 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.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM 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_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover 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.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover 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.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DsspMover method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.Mover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover 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.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot 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.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop 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.PrepackMover 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.SecretionOptimizationMover 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.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover 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.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputter method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover 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.IdealizeHelicesMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax 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.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover 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.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover 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_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManager method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_Ts4 method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover 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.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover 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.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover 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.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.star.StarAbinitio 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.SideChainCopier method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler 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.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover 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.monte_carlo.StepWiseMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.NCSResMapping method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.STMStoredTask method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleResidueInvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDistSasaCalculator method) (pyrosetta.rosetta.utility.tag.Tag method) (pyrosetta.rosetta.utility.tag.XMLSchemaRepeatableCTNode method) get_semi_energy_dist() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_semi_prob_dist() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_semirotameric() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_separated_interface_energy() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_separated_interface_energy_ratio() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_seq_design_options() (in module pyrosetta.rosetta.protocols.antibody.design) get_seq_names() (pyrosetta.rosetta.core.sequence.SequenceFactory method) get_seq_recovery_cache() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver method) get_seq_sep() (in module pyrosetta.rosetta.core.scoring.hbonds) get_seq_sep_scale() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) get_seqpos() (pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue method) get_seqpos1() (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) get_seqpos2() (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) get_sequence() (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.sequence.SequenceFactory method) (pyrosetta.rosetta.protocols.frag_picker.CSTalosIO method) (pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesSeqRecoveryCache method) get_sequence_alignment_cut_max() (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) get_sequence_information() (in module pyrosetta.rosetta.core.import_pose) get_sequence_len() (in module pyrosetta.rosetta.core.pose) get_sequence_profile() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) get_sequence_recovery() (pyrosetta.rosetta.protocols.pose_metric_calculators.SequenceComparison method) get_sequence_region() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) get_session_mysql() (pyrosetta.rosetta.utility.sql_database.DatabaseSessionManager method) get_session_postgres() (pyrosetta.rosetta.utility.sql_database.DatabaseSessionManager method) get_session_sqlite3() (pyrosetta.rosetta.utility.sql_database.DatabaseSessionManager method) get_set_tm_helical() (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) get_sfxn() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) get_sfxn_cycles() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) get_sfxn_name() (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) get_sha1_hash_excluding_chain() (in module pyrosetta.rosetta.core.pose) get_sha1_hash_excluding_chains() (in module pyrosetta.rosetta.core.pose) get_sha1_hash_from_chain() (in module pyrosetta.rosetta.core.pose) get_sha1_hash_from_chains() (in module pyrosetta.rosetta.core.pose) get_shared_silent_data() (pyrosetta.rosetta.core.io.silent.SilentFileData method) get_sheet_antiparallel_info() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_sheet_id() (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFragment method) get_shell_radius() (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) get_shift() (pyrosetta.rosetta.protocols.frag_picker.CSTalosIO method) get_short_backrub_mover() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_short_name_to_iupac_strings_map() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager static method) get_shortest_among_4() (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) get_show_extended() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) get_sid_cutoff_cdr() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity method) get_sid_cutoff_fr() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity method) get_side1_nres() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_side1_score() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_side2_nres() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_side2_score() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_side_from_num() (in module pyrosetta.rosetta.core.chemical.rna) get_sidechain_indices() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper method) get_sidechain_reference_frame() (in module pyrosetta.rosetta.core.pose.motif) get_sidechain_reference_frame_atomids() (in module pyrosetta.rosetta.core.pose.motif) get_sidechain_reference_frame_atomids_with_downstream() (in module pyrosetta.rosetta.core.pose.motif) get_silent_energies() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) get_silent_energy() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) get_silent_file_tags() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) get_silent_struct() (pyrosetta.rosetta.core.io.silent.SilentStructFactory method) get_silent_struct_in() (pyrosetta.rosetta.core.io.silent.SilentStructFactory method) get_silent_struct_out() (pyrosetta.rosetta.core.io.silent.SilentStructFactory method) get_simple_metric() (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects method) get_simple_node() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) get_single_atom_energies() (in module pyrosetta.rosetta.core.scoring) get_single_chain() (pyrosetta.rosetta.core.kinematics.jacobian.JacobianStructure method) get_single_pcs_vec() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) get_single_pre_weighting_scheme() (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingleSet method) get_single_rdc_vec() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingleSet method) get_single_rdc_weighting_scheme() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingleSet method) get_single_rotamer_born_radii() (pyrosetta.rosetta.core.scoring.facts.FACTSPotential method) get_single_rotamer_effective_radii() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) get_size() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.fragment.rna.TorsionSet method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HPool_RMSD method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFragment method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandFragment method) (pyrosetta.rosetta.protocols.pockets.SmallMol method) (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) get_size_sandwich_PK_id() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_skip_low_temp_phase() (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) get_slice_width() (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) get_slide_axis() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_slide_glycan_into_contact() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) get_slide_info() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) get_slide_order() (pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo method) get_slide_threshold() (pyrosetta.rosetta.protocols.symmetry.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SymmetrySlider method) get_slide_type() (pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo method) get_SlideCriteriaType() (pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo method) get_SlideCriteriaVal() (pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo method) get_slope() (pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction method) get_sm_data() (in module pyrosetta.rosetta.core.simple_metrics) get_small_frag_file() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) get_small_frag_size() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) get_smallest_glycan_tree_layer() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_smooth() (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) get_SmoothEnvPairPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_smoothing() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) get_sol_secondary_struct() (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) get_sol_value() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) get_solution_picker() (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) get_solutions() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) get_solvation() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_source() (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionChainEnd method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionLastResidue method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPDB method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPoseNum method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionRefPose method) get_source_pose() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseSegment method) (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) get_source_pose_op() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) get_spanfile() (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover method) get_spanfiles() (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) get_spans() (pyrosetta.rosetta.core.conformation.membrane.SpanningTopology method) get_sparse_aa_info() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) get_sparse_aa_info_for_edge() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) get_sparse_aa_neighbor_info() (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) get_sparse_mat_info_for_curr_state() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) get_sparse_mat_info_for_state() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) get_special_region() (pyrosetta.rosetta.protocols.simple_pose_metric_calculators.NumberHBondsCalculator method) get_species() (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) get_specific() (pyrosetta.rosetta.cppdb.session method) (pyrosetta.rosetta.utility.sql_database.session method) get_specific_atom_coordinate() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) get_specific_element() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManagerStorageMatrix method) get_specific_module_name_as_it_appears_in_xsd() (in module pyrosetta.rosetta.utility.xsd_util) get_spectrum() (in module pyrosetta.rosetta.protocols.electron_density) get_sphere_aa() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) get_spheres() (pyrosetta.rosetta.core.scoring.packstat.SimplePDB method) get_spin_center() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) get_spin_coordinates() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) get_spinlabel() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) get_spinlabel_data() (pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseHandler method) get_spinlabel_data_table() (pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseHandler method) get_spinlabel_site_rsd() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) get_spinsAB() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingle method) get_SplitUnfoldedTwoBodyPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_ss() (pyrosetta.rosetta.protocols.pose_metric_calculators.RotamerRecovery method) get_ss_cutoff() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) get_ss_defaults() (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) get_ss_elements() (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergy method) (pyrosetta.rosetta.protocols.simple_ddg.SSElementBisectddGFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSElementLengthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSElementMotifContactFilter method) get_ss_lowstrand() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) get_ss_names() (pyrosetta.rosetta.core.io.silent.SilentStructFactory method) get_ss_settings() (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) get_ss_type() (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) get_ssbond_record() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) get_ssdep_weight() (in module pyrosetta.rosetta.core.scoring.hbonds) get_SSelements_in_contact() (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergy method) (pyrosetta.rosetta.protocols.simple_filters.SSElementMotifContactFilter method) get_stability_metric() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_stage1_perturb_glycan_com_rot_mag() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) get_stage1_perturb_glycan_com_trans_mag() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) get_stage1_rotate_glycan_about_com() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) get_stage1_torsion_uniform_pert_mag() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) get_stage2_rot_mag() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) get_stage2_trans_mag() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) get_start() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.numeric.interpolation.spline.CubicSpline method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFragment method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandFragment method) get_start_node_vital_segments() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_start_points() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_start_positions() (pyrosetta.rosetta.protocols.helix_capper.HelixNCapperMover method) get_start_res() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) get_start_res_vec() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_start_temperature() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_start_with_current() (pyrosetta.rosetta.core.pack.annealer.DebuggingAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FASTERAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbCoupledRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbLinkingRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbPwatSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.MultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.annealer.RotamerAssigningAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SequenceSymmetricAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SimAnnealerBase method) (pyrosetta.rosetta.core.pack.annealer.SmartFixbbSimAnnealer method) (pyrosetta.rosetta.protocols.flexpack.annealer.FlexbbSimAnnealer method) get_starting_pose() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) get_starting_res_for_connecting_strands() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_starting_residue() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseSegment method) get_starting_z() (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) get_starts_and_ends() (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) get_state_ind_for_this_aa_type() (pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex method) get_state_offset_for_aatype() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) get_state_offset_for_bb() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) get_state_offset_for_restype_group() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) get_statement() (pyrosetta.rosetta.cppdb.backend.connection method) get_states_on_curr_bb() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) get_static_int() (pyrosetta.PythonPyExitCallback static method) (pyrosetta.rosetta.utility.py.PyExitCallback static method) get_static_string() (pyrosetta.PythonPyExitCallback static method) (pyrosetta.rosetta.utility.py.PyExitCallback static method) get_static_string_const() (pyrosetta.PythonPyExitCallback static method) (pyrosetta.rosetta.utility.py.PyExitCallback static method) get_std_dev() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_steal_large_frags() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) get_steal_small_frags() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) get_stem_movemap() (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) get_stem_residues() (pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler method) get_stem_taskfactory() (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) get_step() (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) get_stepsize() (pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) get_stepsize_angle() (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) get_stepsize_z() (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) get_stop_res() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) get_str() (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_string_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t method) get_str_str_data() (pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule method) get_strand_dist_cutoff() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) get_strand_id() (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFragment method) get_strand_pairings() (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing static method) get_strand_pairs() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) get_strand_residue_pairs() (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing static method) get_strand_sew_models_from_db() (in module pyrosetta.rosetta.protocols.legacy_sewing) get_stretch_strand_dist_cutoff() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) get_strict_dssp_changes() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_strict_loops() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) get_stride() (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) get_string() (in module pyrosetta.rosetta.utility.json_spirit) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.utility_exit_detail.Stringifier method) (pyrosetta.rosetta.utility_exit_detail.Stringy method) get_string_comparison_type_strings() (in module pyrosetta.rosetta.protocols.simple_filters) get_string_from_property() (pyrosetta.rosetta.core.chemical.ResidueProperties static method) get_string_from_variant() (pyrosetta.rosetta.core.chemical.ResidueProperties static method) get_string_metric_data() (pyrosetta.rosetta.core.simple_metrics.SimpleMetricData method) get_string_option() (in module pyrosetta.rosetta.basic.options) get_string_or_empty() (in module pyrosetta.rosetta.utility.json_spirit) get_string_property() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) get_string_real_pairs() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) get_string_real_pairs_from_current_job() (in module pyrosetta.rosetta.protocols.jd2) get_string_resnums() (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) get_string_string_pairs() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) get_string_string_pairs_from_current_job() (in module pyrosetta.rosetta.protocols.jd2) get_string_value() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) get_string_vector_option() (in module pyrosetta.rosetta.basic.options) get_strings() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) get_strings_from_current_job() (in module pyrosetta.rosetta.protocols.jd2) get_struct() (pyrosetta.rosetta.protocols.wum.SilentStructStore method) get_struct_id() (pyrosetta.rosetta.protocols.features.StructureFeatures method) get_struct_id1() (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSQLite method) get_struct_id_with_highest_score_from_job_data() (in module pyrosetta.rosetta.protocols.features) get_struct_id_with_highest_score_from_score_data() (in module pyrosetta.rosetta.protocols.features) get_struct_id_with_lowest_score_from_job_data() (in module pyrosetta.rosetta.protocols.features) get_struct_id_with_lowest_score_from_score_data() (in module pyrosetta.rosetta.protocols.features) get_struct_id_with_nth_lowest_score_from_job_data() (in module pyrosetta.rosetta.protocols.features) get_struct_id_with_nth_lowest_score_from_score_data() (in module pyrosetta.rosetta.protocols.features) get_struct_random() (pyrosetta.rosetta.protocols.wum.SilentStructStore method) get_structure() (pyrosetta.rosetta.core.io.silent.SilentFileData method) get_structure_input_tag() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) get_structure_tag() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) get_stub() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyCalciumMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyInterModelMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyPartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorer method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) get_stub1() (pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData method) get_stub2() (pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData method) get_stub3() (pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData method) get_stub_from_residue() (in module pyrosetta.rosetta.core.conformation) get_stub_scorefxn() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) get_stub_stub() (in module pyrosetta.rosetta.core.pose.rna) get_stub_transform() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) get_stubRMSD() (pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop method) get_sub_score() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) get_sub_score_exclude_res() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) get_subbin_type_from_name() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) get_subbin_type_name() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) get_subcluster() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) get_submotif_moves() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.submotif.SubMotifLibrary method) get_subpose() (in module pyrosetta.rosetta.core.pose.symmetry) get_subset() (pyrosetta.rosetta.core.scoring.MembraneTopology method) (pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset method) get_subset_from_residues() (in module pyrosetta.rosetta.core.select) get_subset_name() (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) get_substituents_to_ring_atom() (pyrosetta.rosetta.core.conformation.Residue method) get_substrate_foldtree() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) get_subunit_name_to_component() (in module pyrosetta.rosetta.core.pose.symmetry) (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) get_subunit_num_to_virt_id() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_subunits() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_success() (pyrosetta.rosetta.protocols.LoopRebuild method) get_sugar_centroid() (in module pyrosetta.rosetta.core.pose.rna) get_sugar_donor() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) get_sugar_env_score() (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) get_sugar_pucker_distr() (in module pyrosetta.rosetta.core.scoring.dna) get_sugar_torsion_mean_and_sdev() (pyrosetta.rosetta.core.scoring.dna.DNA_DihedralPotential method) get_sugar_torsions() (in module pyrosetta.rosetta.core.scoring.dna) get_sugars_to_preglycosylate() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) get_suite_torsion_ids() (in module pyrosetta.rosetta.core.pose.rna) get_sum_water_weight_grid() (pyrosetta.rosetta.core.energy_methods.WaterWeightGridSet method) get_summary_type_strings() (in module pyrosetta.rosetta.core.simple_metrics.metrics) get_super_secret_fixed_interface_mode() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_superposition_transformation() (in module pyrosetta.rosetta.protocols.hybridization) get_surf_tot() (in module pyrosetta.rosetta.core.scoring.packing) get_surf_vol() (in module pyrosetta.rosetta.core.scoring.packing) get_surf_vol_deriv() (in module pyrosetta.rosetta.core.scoring.packing) get_surface_area() (pyrosetta.rosetta.core.scoring.packstat.LeeRichards method) get_surface_esp() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) get_surrounding_O2prime_hydrogen() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) get_svd_solution() (pyrosetta.rosetta.basic.svd.SVD_Solver method) get_svm() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorSVM method) get_sw_can_by_sh_id() (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFragment method) get_sym_aware_jump_num() (in module pyrosetta.rosetta.core.pose.symmetry) get_sym_dof_names() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) get_symbols() (pyrosetta.rosetta.core.sequence.ABEGOManager method) get_symdof_subunits() (in module pyrosetta.rosetta.core.pose.symmetry) get_symm_axis() (in module pyrosetta.rosetta.core.pose.symmetry) get_symm_data() (pyrosetta.rosetta.protocols.topology_broker.claims.SymmetryClaim method) get_symm_info() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) get_symmetry_name() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_symmetry_type() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_symmin_ig_owner() (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) get_symmlinmem_ig_owner() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) get_symmlinmem_node() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) get_symmMap() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) get_symmops_Aba2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Abm2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Ama2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Amm2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_B11m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_C121() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_C12slashc1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_C12slashm1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_C1c1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_C1m1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_C222() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_C2221() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Ccc2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Ccca__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Cccm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Cmc21() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Cmca() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Cmcm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Cmm2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Cmma() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Cmmm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_F222() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_F23() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_F4132() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_F432() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fdd2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fddd__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fdminus3__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fdminus3c__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fdminus3m__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fminus43c() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fminus43m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fmm2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fmminus3() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fmminus3c() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fmminus3m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Fmmm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I212121() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I213() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I222() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I23() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I4() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I41() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I4122() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I4132() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I41cd() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I41md() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I41slasha__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I41slashacd__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I41slashamd__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I422() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I432() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I4cm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I4mm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I4slashm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I4slashmcm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_I4slashmmm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Iaminus3() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Iaminus3d() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Iba2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Ibam() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Ibca() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Ima2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Iminus4() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Iminus42d() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Iminus42m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Iminus43d() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Iminus43m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Iminus4c2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Iminus4m2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Imm2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Imma() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Imminus3() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Imminus3m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Immm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P121() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P1211() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P121slashc1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P121slashm1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P121slashn1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P12slashc1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P12slashm1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P1c1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P1m1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P21212() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P212121() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P213() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P222() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P2221() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P23() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P3() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P31() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P3112() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P312() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P3121() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P31c() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P31m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P32() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P321() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P3212() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P3221() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P3c1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P3m1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P41() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P41212() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4122() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4132() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4212() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P422() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42212() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4222() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4232() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42bc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42cm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42mc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42nm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42slashm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42slashmbc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42slashmcm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42slashmmc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42slashmnm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42slashn__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42slashnbc__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42slashncm__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42slashnmc__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P42slashnnm__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P43() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P432() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P43212() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4322() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4332() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4bm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4cc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4mm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4nc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4slashm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4slashmbm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4slashmcc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4slashmmm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4slashmnc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4slashn__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4slashnbm__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4slashncc__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4slashnmm__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P4slashnnc__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P61() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6122() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P62() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P622() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6222() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P63() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6322() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P63cm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P63mc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P63slashm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P63slashmcm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P63slashmmc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P64() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6422() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P65() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6522() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6cc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6mm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6slashm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6slashmcc() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_P6slashmmm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Paminus3() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pba2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pbam() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pban__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pbca() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pbcm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pbcn() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pca21() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pcc2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pcca() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pccm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pccn() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pma2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pmc21() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus3() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus31c() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus31m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus3c1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus3m1() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus4() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus421c() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus421m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus42c() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus42m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus43m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus43n() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus4b2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus4c2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus4m2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus4n2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus6() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus62c() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus62m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus6c2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pminus6m2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pmm2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pmma() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pmminus3() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pmminus3m() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pmminus3n() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pmmm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pmmn__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pmn21() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pmna() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pna21() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pnc2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pnma() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pnminus3__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pnminus3m__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pnminus3n__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pnn2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pnna() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pnnm() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Pnnn__2() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_R32__H() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_R3__H() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_R3c__H() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_R3m__H() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Rminus3__H() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Rminus3c__H() (in module pyrosetta.rosetta.protocols.cryst) get_symmops_Rminus3m__H() (in module pyrosetta.rosetta.protocols.cryst) get_t() (pyrosetta.rosetta.protocols.hybridization.TMalign method) get_T_xx() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) get_T_xy() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) get_T_xz() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) get_T_yy() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) get_T_yz() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) get_table_size() (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t method) get_tag() (in module pyrosetta.rosetta.core.io.rna) (in module pyrosetta.rosetta.protocols.features.strand_assembly) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HPool_RMSD method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.Pool_RMSD method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.toolbox.KClusterData method) get_tag_and_silent_file_for_struct() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) get_tag_from_pdb_filename() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) get_tag_list() (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) get_tag_name() (in module pyrosetta.rosetta.utility.xsd_util) get_tag_residue_number() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSMultiSet method) get_tag_score_map() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) get_tags() (in module pyrosetta.rosetta.core.io.rna) get_tail_node() (pyrosetta.rosetta.protocols.jd3.JobDirectedEdge method) (pyrosetta.rosetta.utility.graph.DirectedEdge method) get_tail_node_ind() (pyrosetta.rosetta.protocols.jd3.JobDirectedEdge method) (pyrosetta.rosetta.utility.graph.DirectedEdge method) get_tailfunction_from_name() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup method) get_tailfunction_name() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup method) get_target_atom_name() (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) get_target_attractive_weight() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) get_target_position_map_make_dna_mutations() (in module pyrosetta.rosetta.protocols.motifs) get_target_positions_make_dna_mutations() (in module pyrosetta.rosetta.protocols.motifs) get_target_repulsive_weight() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) get_target_residue() (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) get_target_sequences() (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) get_targetconformers_user() (in module pyrosetta.rosetta.protocols.motifs) get_targeted_sequence() (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) get_task() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.task_operations.STMStoredTask method) get_task_factory() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) get_task_operation() (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects method) get_task_operation_names_from_xsd() (in module pyrosetta.rosetta.utility.xsd_util) get_task_operations() (in module pyrosetta.rosetta.core.pack.task) get_TaskFactory_AllCDRs() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_TaskFactory_OneCDR() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_tau_c() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) get_tau_c_max() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) get_tau_c_min() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) get_tau_e() (pyrosetta.rosetta.core.io.nmr.ParaIon method) get_tau_r() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) get_tau_t() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) get_temp() (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) get_temp_cycles() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) get_temperature() (pyrosetta.rosetta.core.pack.annealer.DebuggingAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FASTERAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbCoupledRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbLinkingRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbPwatSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.MultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.annealer.RotamerAssigningAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SequenceSymmetricAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SimAnnealerBase method) (pyrosetta.rosetta.core.pack.annealer.SmartFixbbSimAnnealer method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.flexpack.annealer.FlexbbSimAnnealer method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) (pyrosetta.rosetta.protocols.md.Thermostat method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_template() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerLinks method) (pyrosetta.rosetta.protocols.abinitio.Templates method) get_template_atoms_at_pos() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) get_tenA_neighbor_residues() (in module pyrosetta.rosetta.core.select) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) get_tensor() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) get_tensor_const() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) get_tensorflow_compilation_instructions() (in module pyrosetta.rosetta.basic.tensorflow_manager) get_terminal_segments() (pyrosetta.rosetta.protocols.sewing.hashing.EdgeMapGenerator method) get_terminal_varianttypes() (in module pyrosetta.rosetta.core.chemical) get_termini_from_pose() (in module pyrosetta.rosetta.protocols.sic_dock) get_terminus() (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) get_testing_phase() (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) get_third_atom() (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) get_third_offset() (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) get_this_filter_type_name() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) get_thresh() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorMatrix method) get_threshold() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) get_throw_on_fail() (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) get_time() (in module pyrosetta.rosetta.protocols.wum) get_timer() (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) get_tips() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) get_tm_alpha() (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) get_TMscore() (pyrosetta.rosetta.core.scoring.TMscore method) get_tna_suite_potential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_token() (in module pyrosetta.rosetta.core.pack.task) get_tol() (pyrosetta.rosetta.protocols.nmr.pre.PREDistanceRecord method) get_tolerance() (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) get_top_designs() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) get_top_N_filter() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) get_torID() (pyrosetta.rosetta.protocols.normalmode.NormalMode method) get_torsion() (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) get_torsion_angle_atom_ids() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) get_torsion_bin() (in module pyrosetta.rosetta.core.conformation) get_torsion_id() (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) get_torsion_ids() (pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1 method) (pyrosetta.rosetta.core.scoring.rna.TNA_SuitePotential method) get_torsion_mean() (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) get_torsion_sd() (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) get_torsion_type() (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler2D method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler3D method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerND method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) get_torsion_values() (pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1 method) get_TorsionID() (pyrosetta.rosetta.core.optimization.CartesianMinimizerMap method) get_torsions() (in module pyrosetta.rosetta.protocols.recces) (in module pyrosetta.rosetta.protocols.recces.scratch) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) get_torsions_for_all_solutions() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) get_total() (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) get_total_base_axis_score() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) get_total_base_pair_score() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) get_total_base_stack_axis_score() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) get_total_base_stack_score() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) get_total_base_stagger_score() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) get_total_dots() (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) get_total_energy_in_curr_state_assignment_for_all_states() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) get_total_exp_chemical_shift_data_points() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential method) get_total_frames() (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) get_total_Hbond_E() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_total_hbonds() (pyrosetta.rosetta.protocols.simple_pose_metric_calculators.NumberHBondsCalculator method) get_total_hsasa() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_total_hsasa_bb() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_total_hsasa_sc() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_total_mutation_sets() (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) get_total_num_CDRs() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) get_total_number_pcs() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSData method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSMultiSet method) get_total_number_pre() (pyrosetta.rosetta.core.scoring.nmr.pre.PREData method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) get_total_number_rdc() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCData method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) get_total_rel_hsasa() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_total_rounds_for_overlap_one_layer_two() (in module pyrosetta.rosetta.protocols.carbohydrates) get_total_sasa() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_total_sasa_bb() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_total_sasa_sc() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) get_total_score() (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) get_total_size() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector method) get_totalE() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) get_totals_columns() (pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t method) get_touched_res() (in module pyrosetta.rosetta.protocols.mpi_refinement) get_trans_dofs() (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) get_trans_mag() (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) get_trans_magnitude() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) get_trans_step() (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) get_transaction_mode() (pyrosetta.rosetta.utility.sql_database.session method) get_transformation() (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) get_translation() (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.RT method) get_translation_magnitude() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) get_translation_matrix() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_tree() (in module pyrosetta.rosetta.core.import_pose) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_tree_containing_residue() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_tree_map() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_tree_root_of_glycan_residue() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_tree_start_of_glycan_residue() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) get_trie() (pyrosetta.rosetta.core.conformation.RotamerSetBase method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) get_trim_terminal_loops() (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) get_trRosetta_neural_net_citation() (pyrosetta.rosetta.protocols.trRosetta.trRosettaProtocol_v1 static method) get_twist() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) get_two_body_energies_for_relaxed_states() (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) get_two_body_energy() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) get_two_body_energy_for_edge() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) get_two_body_energy_smi() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) get_two_body_table_size() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) get_type() (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop 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.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.buns.BuriedUnsatHbondFilter2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.ConservedPosMutationFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder 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.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreCutoffFilter method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.constraint_filters.ShowConstraintsFilter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) (pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter 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.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover 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.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.dna_dock.DNAClashCheckFilter method) (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilter method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilter method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.LigBurialFilter method) (pyrosetta.rosetta.protocols.enzdes.LigDSasaFilter method) (pyrosetta.rosetta.protocols.enzdes.LigInterfaceEnergyFilter method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.RemoveLigandFilter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.RepackWithoutLigandFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CalculatorFilter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.ContingentFilter method) (pyrosetta.rosetta.protocols.filters.FalseFilter method) (pyrosetta.rosetta.protocols.filters.Filter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.filters.ReplicateFilter method) (pyrosetta.rosetta.protocols.filters.StochasticFilter method) (pyrosetta.rosetta.protocols.filters.TimeFilter method) (pyrosetta.rosetta.protocols.filters.TrueFalseFilter method) (pyrosetta.rosetta.protocols.filters.TrueFilter method) (pyrosetta.rosetta.protocols.filters.VectorPoseFilter method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.filters.CoreDunbrackFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.FragQualFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.InterlockingAromaFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.NcontactsFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.ParallelBetaPairingPreferenceFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureCountFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureHasResidueFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol 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.filters.ConstraintFulfilmentFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ScorePoseSegmentFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.forge.components.BDR 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.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetScore method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) (pyrosetta.rosetta.protocols.hydrate.Hydrate method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilter method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilter method) (pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilter method) (pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilter method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilter method) (pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilter method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover 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.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM 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_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilter method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover 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.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover 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.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DsspMover method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.Mover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.PyMOLObserver method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.network.UIObserver method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorer method) (pyrosetta.rosetta.protocols.pose_sewing.filters.HasDisulfideFilter method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AtomicContactCountFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AverageDegreeFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.ClashWithTargetFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FNatFilter 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.InterfaceHolesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.IRmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.LRmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdSimpleFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SpecificResiduesNearInterfaceFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SSamountFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreLoopsFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.Torsion method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover 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.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot 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.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop 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.PrepackMover 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.SecretionOptimizationMover 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.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover 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.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.qsarPoint method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover 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.IdealizeHelicesMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.FitnessFilter method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax 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.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover 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.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover 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_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.score_filters.GeometryFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreTypeFilter method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSewingResidue method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.simple_ddg.AlaScan method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScan method) (pyrosetta.rosetta.protocols.simple_ddg.InterfaceBindingEnergyDensityFilter method) (pyrosetta.rosetta.protocols.simple_ddg.SSElementBisectddGFilter method) (pyrosetta.rosetta.protocols.simple_filters.AbinitioBaseFilter method) (pyrosetta.rosetta.protocols.simple_filters.AngleToVector method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.AveragePathLengthFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.COFilter method) (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter method) (pyrosetta.rosetta.protocols.simple_filters.DisulfideEntropyFilter method) (pyrosetta.rosetta.protocols.simple_filters.DomainInterfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.EnergyPerResidueFilter method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_filters.ExpiryFilter method) (pyrosetta.rosetta.protocols.simple_filters.FileExistFilter method) (pyrosetta.rosetta.protocols.simple_filters.FileRemoveFilter method) (pyrosetta.rosetta.protocols.simple_filters.HelixHelixAngleFilter method) (pyrosetta.rosetta.protocols.simple_filters.HolesFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHydrophobicResidueContactsFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceSasaFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterRepeatContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.IntraRepeatContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MembAccesResidueLipophilicityFilter method) (pyrosetta.rosetta.protocols.simple_filters.MotifScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.MPSpanAngleFilter method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilter method) (pyrosetta.rosetta.protocols.simple_filters.NeighborTypeFilter method) (pyrosetta.rosetta.protocols.simple_filters.NetChargeFilter method) (pyrosetta.rosetta.protocols.simple_filters.NMerPSSMEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.NMerSVMEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.NonSequentialNeighborsFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackStatFilter method) (pyrosetta.rosetta.protocols.simple_filters.PDDFScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.RangeFilter method) (pyrosetta.rosetta.protocols.simple_filters.ReadPoseExtraScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.RepeatParameterFilter method) (pyrosetta.rosetta.protocols.simple_filters.ReportFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueBurialFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueChiralityFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueIEFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueLipophilicityFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSelectionDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSetChainEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResiduesInInterfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.RGFilter method) (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter method) (pyrosetta.rosetta.protocols.simple_filters.SAXSScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) (pyrosetta.rosetta.protocols.simple_filters.SheetFilter method) (pyrosetta.rosetta.protocols.simple_filters.SidechainRmsdFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) (pyrosetta.rosetta.protocols.simple_filters.SpanTopologyMatchPoseFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSElementLengthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSElementMotifContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinder method) (pyrosetta.rosetta.protocols.simple_filters.StemFinder method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareSASAFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter method) (pyrosetta.rosetta.protocols.simple_filters.TerminusDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.TMsAACompFilter method) (pyrosetta.rosetta.protocols.simple_filters.TMsSpanMembraneFilter method) (pyrosetta.rosetta.protocols.simple_filters.TotalSasaFilter method) (pyrosetta.rosetta.protocols.simple_filters.Worst9merFilter method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover 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.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover 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.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover 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.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.star.StarAbinitio 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.SideChainCopier method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler 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.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover 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.monte_carlo.StepWiseMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) get_type_difference_name() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData static method) get_type_info() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeMap method) get_type_name() (in module pyrosetta.rosetta.utility.xsd_util) get_u() (pyrosetta.rosetta.protocols.hybridization.TMalign method) get_ub_function_cutoff() (pyrosetta.rosetta.numeric.interpolation.spline.CompoundInterpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.Interpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.SimpleInterpolator method) get_ub_function_intercept() (pyrosetta.rosetta.numeric.interpolation.spline.CompoundInterpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.Interpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.SimpleInterpolator method) get_ub_function_slope() (pyrosetta.rosetta.numeric.interpolation.spline.CompoundInterpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.Interpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.SimpleInterpolator method) get_ubdy() (pyrosetta.rosetta.numeric.interpolation.spline.SplineGenerator method) get_UBQpdb() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) get_ubx() (pyrosetta.rosetta.numeric.interpolation.spline.SplineGenerator method) get_uby() (pyrosetta.rosetta.numeric.interpolation.spline.SplineGenerator method) get_ui_observer() (in module pyrosetta.rosetta.protocols.network) get_uint64() (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_string_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t method) get_unaligned() (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) get_unbound_mode() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_unbound_mut_pose() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) get_unbound_wt_pose() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) get_undefined_real() (in module pyrosetta.rosetta.utility) get_undefined_size() (in module pyrosetta.rosetta.utility) get_UnfoldedStatePotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_unfoled_potential_file_weights() (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential method) get_uniform_backrub() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover method) get_unique_connection_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) get_unique_sequences() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) get_unrecognized_atoms() (pyrosetta.rosetta.core.pose.PDBInfo method) get_unrecognized_res_name() (pyrosetta.rosetta.core.pose.PDBInfo method) get_unrecognized_res_size() (pyrosetta.rosetta.core.pose.PDBInfo method) get_unrelaxed_pose() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) get_unsats_for_mres() (pyrosetta.rosetta.protocols.hbnet.NetworkState method) get_unseen_score() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorExternal method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded method) get_unweighted_score_term() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_update() (pyrosetta.rosetta.protocols.stepwise.legacy.screener.ProteinAtrRepScreener method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.RNA_AtrRepScreener method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.SimplePoseSelection method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.SimpleRMSD_Screener method) (pyrosetta.rosetta.protocols.stepwise.screener.AlignRMSD_Screener method) (pyrosetta.rosetta.protocols.stepwise.screener.AnchorSugarScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.BaseBinMapUpdater method) (pyrosetta.rosetta.protocols.stepwise.screener.BaseCentroidScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.BulgeApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.CentroidDistanceScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.FastForwardToNextResidueAlternative method) (pyrosetta.rosetta.protocols.stepwise.screener.FastForwardToNextRigidBody method) (pyrosetta.rosetta.protocols.stepwise.screener.IntegrationTestBreaker method) (pyrosetta.rosetta.protocols.stepwise.screener.O2PrimeScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PackScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PartitionContactScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PhosphateScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PoseSelectionScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.ProteinCCD_ClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.ResidueContactScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryResidueBasedScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryStubBasedScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.SampleApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.Scorer method) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseResiduePairScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.StubApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.StubDistanceScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.SugarInstantiator method) (pyrosetta.rosetta.protocols.stepwise.screener.TagDefinition method) (pyrosetta.rosetta.protocols.stepwise.screener.VDW_BinScreener method) get_update_boinc() (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) get_upper_bound_dy() (pyrosetta.rosetta.core.scoring.func.SplineFunc method) get_upper_bound_x() (pyrosetta.rosetta.core.scoring.func.SplineFunc method) get_upper_bound_y() (pyrosetta.rosetta.core.scoring.func.SplineFunc method) get_upper_cutpoint_partner_for_lower() (in module pyrosetta.rosetta.core.scoring.methods) get_upper_fasta() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) get_upper_pose() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) get_upstream_chain() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) get_upstream_restype() (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) get_usage_from_procfilesystem() (in module pyrosetta.rosetta.basic) get_use_centroid_dG() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) get_use_contact_selector() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_use_custom_dihedral_angle() (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) get_use_input_set_selector() (pyrosetta.rosetta.protocols.residue_selectors.HBondSelector method) get_use_ligand_selector() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) get_use_lowest() (pyrosetta.rosetta.protocols.frag_picker.scores.ABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) get_use_symmetry() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) get_use_tracer() (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) get_useful_HOH_coords() (in module pyrosetta.rosetta.protocols.magnesium) get_user_defined_name() (pyrosetta.rosetta.protocols.buns.BuriedUnsatHbondFilter2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.ConservedPosMutationFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreCutoffFilter method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.constraint_filters.ShowConstraintsFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter method) (pyrosetta.rosetta.protocols.dna_dock.DNAClashCheckFilter method) (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter method) (pyrosetta.rosetta.protocols.enzdes.LigBurialFilter method) (pyrosetta.rosetta.protocols.enzdes.LigDSasaFilter method) (pyrosetta.rosetta.protocols.enzdes.LigInterfaceEnergyFilter method) (pyrosetta.rosetta.protocols.enzdes.RemoveLigandFilter method) (pyrosetta.rosetta.protocols.enzdes.RepackWithoutLigandFilter 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.CalculatorFilter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.ContingentFilter method) (pyrosetta.rosetta.protocols.filters.FalseFilter method) (pyrosetta.rosetta.protocols.filters.Filter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.filters.ReplicateFilter method) (pyrosetta.rosetta.protocols.filters.StochasticFilter method) (pyrosetta.rosetta.protocols.filters.TimeFilter method) (pyrosetta.rosetta.protocols.filters.TrueFalseFilter method) (pyrosetta.rosetta.protocols.filters.TrueFilter method) (pyrosetta.rosetta.protocols.filters.VectorPoseFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.CoreDunbrackFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.FragQualFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.InterlockingAromaFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.NcontactsFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.ParallelBetaPairingPreferenceFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureCountFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureHasResidueFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ConstraintFulfilmentFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ScorePoseSegmentFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.hbnet.HBNetScore method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilter method) (pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilter method) (pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilter method) (pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilter method) (pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilter method) (pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilter method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilter method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorer method) (pyrosetta.rosetta.protocols.pose_sewing.filters.HasDisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AtomicContactCountFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AverageDegreeFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.ClashWithTargetFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FNatFilter 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.InterfaceHolesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.IRmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.LRmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdSimpleFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SpecificResiduesNearInterfaceFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SSamountFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreLoopsFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.Torsion method) (pyrosetta.rosetta.protocols.recon_design.FitnessFilter method) (pyrosetta.rosetta.protocols.score_filters.GeometryFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreTypeFilter method) (pyrosetta.rosetta.protocols.simple_ddg.AlaScan method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScan method) (pyrosetta.rosetta.protocols.simple_ddg.InterfaceBindingEnergyDensityFilter method) (pyrosetta.rosetta.protocols.simple_ddg.SSElementBisectddGFilter method) (pyrosetta.rosetta.protocols.simple_filters.AbinitioBaseFilter method) (pyrosetta.rosetta.protocols.simple_filters.AngleToVector method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.AveragePathLengthFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.COFilter method) (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter method) (pyrosetta.rosetta.protocols.simple_filters.DisulfideEntropyFilter method) (pyrosetta.rosetta.protocols.simple_filters.DomainInterfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.EnergyPerResidueFilter method) (pyrosetta.rosetta.protocols.simple_filters.ExpiryFilter method) (pyrosetta.rosetta.protocols.simple_filters.FileExistFilter method) (pyrosetta.rosetta.protocols.simple_filters.FileRemoveFilter method) (pyrosetta.rosetta.protocols.simple_filters.HelixHelixAngleFilter method) (pyrosetta.rosetta.protocols.simple_filters.HolesFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHydrophobicResidueContactsFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceSasaFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterRepeatContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.IntraRepeatContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MembAccesResidueLipophilicityFilter method) (pyrosetta.rosetta.protocols.simple_filters.MotifScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.MPSpanAngleFilter method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilter method) (pyrosetta.rosetta.protocols.simple_filters.NeighborTypeFilter method) (pyrosetta.rosetta.protocols.simple_filters.NetChargeFilter method) (pyrosetta.rosetta.protocols.simple_filters.NMerPSSMEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.NMerSVMEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.NonSequentialNeighborsFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackStatFilter method) (pyrosetta.rosetta.protocols.simple_filters.PDDFScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.RangeFilter method) (pyrosetta.rosetta.protocols.simple_filters.ReadPoseExtraScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.RepeatParameterFilter method) (pyrosetta.rosetta.protocols.simple_filters.ReportFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueBurialFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueChiralityFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueIEFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueLipophilicityFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSelectionDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSetChainEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResiduesInInterfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.RGFilter method) (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter method) (pyrosetta.rosetta.protocols.simple_filters.SAXSScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) (pyrosetta.rosetta.protocols.simple_filters.SheetFilter method) (pyrosetta.rosetta.protocols.simple_filters.SidechainRmsdFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) (pyrosetta.rosetta.protocols.simple_filters.SpanTopologyMatchPoseFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSElementLengthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSElementMotifContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinder method) (pyrosetta.rosetta.protocols.simple_filters.StemFinder method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareSASAFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter method) (pyrosetta.rosetta.protocols.simple_filters.TerminusDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.TMsAACompFilter method) (pyrosetta.rosetta.protocols.simple_filters.TMsSpanMembraneFilter method) (pyrosetta.rosetta.protocols.simple_filters.TotalSasaFilter method) (pyrosetta.rosetta.protocols.simple_filters.Worst9merFilter method) get_using_a_resselect() (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) get_valence_electrons_sp() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) get_valid_ramachandran_hashes() (pyrosetta.rosetta.protocols.features.BetaTurnDetection static method) get_valid_resid() (pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) get_Vall() (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager method) get_vall() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) get_vall_by_key() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) get_vall_count() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) get_vall_end_line_by_key() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) get_vall_file() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) get_vall_filename() (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) get_vall_last_residue_key_by_key() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) get_vall_middle_res_id() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) get_vall_provider() (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) get_vall_start_line_by_key() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) get_value() (in module pyrosetta.rosetta.utility.json_spirit) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricData method) (pyrosetta.rosetta.protocols.filters.ContingentFilter method) (pyrosetta.rosetta.protocols.qsar.qsarPoint method) (pyrosetta.rosetta.utility.json_spirit.Config_map_std_basic_string_wchar_t_t static method) (pyrosetta.rosetta.utility.json_spirit.Config_map_std_string_t static method) (pyrosetta.rosetta.utility.json_spirit.Config_vector_std_string_t static method) get_value_list() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) get_values() (pyrosetta.rosetta.numeric.interpolation.spline.BicubicSpline method) (pyrosetta.rosetta.numeric.interpolation.spline.CubicSpline method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) get_variable() (pyrosetta.rosetta.numeric.expression_parser.BooleanExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.SimpleExpressionCreator method) get_variant_from_string() (pyrosetta.rosetta.core.chemical.ResidueProperties static method) get_vary_bondangles() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) get_vary_cutpoints() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) get_vd_to_index() (pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler method) get_VdRdPhi() (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) get_VDW_align_res() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker method) get_VDW_weight() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) get_VdWTinkerPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_vec_AA_kind() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_vec_distinct_sheet_id() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_vec_of_sw_can_by_sh_id() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_vector() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector method) get_vector_exclude_residues() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 method) get_vector_filename() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 method) get_vector_of_loop_AA_distribution() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_vector_of_strand_AA_distribution() (in module pyrosetta.rosetta.protocols.features.strand_assembly) get_vector_weight() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 method) get_version() (pyrosetta.rosetta.core.chemical.ResidueDatabaseIO method) (pyrosetta.rosetta.protocols.sewing.hashing.SegmentVector method) get_vertex() (pyrosetta.rosetta.core.conformation.PointGraphPy method) (pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) get_vertex_member_of_energy_sum_group() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) get_vicinity_degree() (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) get_vicinity_sampling() (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) get_view_in_pymol() (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) get_virt_id_to_subunit_chain() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_virt_id_to_subunit_num() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_virt_id_to_subunit_residue() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_virtual_connects() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_virtual_coordinates() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_virtual_id_to_num() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_virtual_num_to_id() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) get_visited() (pyrosetta.rosetta.protocols.pockets.SmallMol method) get_vital_residues() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) get_vital_selector() (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) get_voxel_coordinates() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) get_voxel_grid() (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelEnsemble method) get_voxel_spacing() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) get_voxel_volume() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) get_w_rep() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) get_watch_in_pymol() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) get_water_builder_for_restype() (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase method) get_water_res() (in module pyrosetta.rosetta.protocols.magnesium) get_water_uniform_rotation_sampler() (in module pyrosetta.rosetta.protocols.magnesium) get_water_weight_grid() (pyrosetta.rosetta.core.energy_methods.WaterWeightGridSet method) get_WaterAdductHBondPotential() (pyrosetta.rosetta.core.scoring.ScoringManager method) get_watson_crick_base_pair_atoms() (in module pyrosetta.rosetta.core.chemical.rna) get_WC_atom() (in module pyrosetta.rosetta.core.chemical.rna) get_wc_near_o2prime() (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential method) get_weight() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.func.CircularSplineFunc method) (pyrosetta.rosetta.core.scoring.func.SplineFunc method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingle method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingle method) (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingleSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingle method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingleSet method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) (pyrosetta.rosetta.protocols.pack_interface.ProteinProteinInterfaceUpweighter method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_per_lanthanides method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_per_lanthanides_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_per_lanthanides_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_per_lanthanides_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 method) (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandAssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorer method) get_weighted_energy() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) get_weighted_energy_with_higher_indexed_nodes() (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) get_weights() (pyrosetta.rosetta.core.scoring.SplitUnfoldedTwoBodyPotential method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) get_weights_for_one_partner_hbonder() (in module pyrosetta.rosetta.core.scoring.hbonds) get_weights_for_two_partner_hbonder() (in module pyrosetta.rosetta.core.scoring.hbonds) get_well_depth() (pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction method) get_win1_dens_zscore() (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) get_win1_denscc() (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) get_win3_dens_zscore() (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) get_win3_denscc() (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) get_window() (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) get_window_at_index() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter method) get_window_width() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) get_work_unit() (pyrosetta.rosetta.protocols.wum.WorkUnitList method) get_work_unit_clone() (pyrosetta.rosetta.protocols.wum.WorkUnitList method) get_working_directory() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) get_wt_adp() (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) get_wt_averaged_score_components() (pyrosetta.rosetta.protocols.ddg.ddGMover method) get_wt_averaged_totals() (pyrosetta.rosetta.protocols.ddg.ddGMover method) get_wt_dens() (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) get_wt_min_score_components() (pyrosetta.rosetta.protocols.ddg.ddGMover method) get_wt_min_totals() (pyrosetta.rosetta.protocols.ddg.ddGMover method) get_wu_type() (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Sampler method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore method) (pyrosetta.rosetta.protocols.wum.DatabaseEntryWorkUnit method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.WorkUnit_Wait method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) get_x() (pyrosetta.rosetta.core.conformation.symmetry.VirtualCoordinate method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover method) get_X_all() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_Ts4 method) get_x_middle() (pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction method) get_xform_score_BB_BB() (pyrosetta.rosetta.core.scoring.motif.MotifHashManager method) get_xform_score_BB_PH() (pyrosetta.rosetta.core.scoring.motif.MotifHashManager method) get_xform_score_BB_PO() (pyrosetta.rosetta.core.scoring.motif.MotifHashManager method) get_xform_score_frags() (pyrosetta.rosetta.core.scoring.motif.MotifHashManager method) get_xform_score_PH_PO() (pyrosetta.rosetta.core.scoring.motif.MotifHashManager method) get_xform_score_SC_BB() (pyrosetta.rosetta.core.scoring.motif.MotifHashManager method) get_xform_score_SC_SC() (pyrosetta.rosetta.core.scoring.motif.MotifHashManager method) get_xform_stats() (in module pyrosetta.rosetta.protocols.sic_dock) get_xml_attributes() (pyrosetta.rosetta.protocols.sewing.requirements.ClashRequirement static method) (pyrosetta.rosetta.protocols.sewing.requirements.KeepLigandContactsRequirement static method) get_xml_schema_attributes() (pyrosetta.rosetta.core.pack.task.operation.ChainIs static method) (pyrosetta.rosetta.core.pack.task.operation.ChainIsnt static method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty static method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIs static method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsnt static method) (pyrosetta.rosetta.core.pack.task.operation.ResidueLacksProperty static method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3Is static method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3Isnt static method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIs static method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsnt static method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoHasLabel static method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoLacksLabel static method) get_xsd_complex_type() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover static method) get_xyz() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) get_xyz_bin() (pyrosetta.rosetta.core.pose.rna.VDW_Grid method) get_y() (pyrosetta.rosetta.core.conformation.symmetry.VirtualCoordinate method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover method) get_Y_all() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_Ts4 method) get_y_axis() (in module pyrosetta.rosetta.core.scoring.dna) get_y_axis_atoms() (in module pyrosetta.rosetta.core.scoring.dna) get_Z_all() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_Ts4 method) get_z_axis() (in module pyrosetta.rosetta.core.scoring.dna) get_ZAP_espGrid_values() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) get_ZAP_espGrid_values_with_type() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) get_zeta_cutoff() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) getAANeighborOffsets() (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t method) getActiveAtom() (pyrosetta.rosetta.RDKit.RWMol method) getAllAtomsWithBookmark() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) getAllBondsWithBookmark() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) getANN_PredError() (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib method) getAtomDegree() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) getAtomicNum() (pyrosetta.rosetta.RDKit.Atom method) getAtomMapNum() (pyrosetta.rosetta.RDKit.Atom method) getAtomMask() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) getAtomPos() (pyrosetta.rosetta.RDKit.Conformer method) GetAtoms() (pyrosetta.rosetta.core.scoring.sc.ContactMolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeSimilarityCalculator method) getAtomWithBookmark() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) getAtomWithIdx() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) getAVG() (in module pyrosetta.rosetta.protocols.sparta) getaxis() (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) getBase() (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) getBeginAtom() (pyrosetta.rosetta.RDKit.Bond method) getBeginAtomIdx() (pyrosetta.rosetta.RDKit.Bond method) getBondAngle() (pyrosetta.rosetta.protocols.sparta.PDB method) getBondBetweenAtoms() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) getBondDir() (pyrosetta.rosetta.RDKit.Bond method) getBondType() (pyrosetta.rosetta.RDKit.Bond method) getBondTypeAsDouble() (pyrosetta.rosetta.RDKit.Bond method) getBondWithBookmark() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) getBondWithIdx() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) getBounds() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) getCachedScore() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) getcenter() (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) getChi1() (pyrosetta.rosetta.protocols.sparta.PDB method) getChi2() (pyrosetta.rosetta.protocols.sparta.PDB method) getChiralTag() (pyrosetta.rosetta.RDKit.Atom method) getConfidence() (pyrosetta.rosetta.protocols.sparta.ANN method) getConformer() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) getContent() (pyrosetta.rosetta.protocols.pockets.SmallMol method) getCoordinateTransformation() (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) getCutoff() (pyrosetta.rosetta.protocols.match.downstream.ScoringSecMatchRPE method) getD() (pyrosetta.rosetta.protocols.cluster.calibur.AdjacentList method) getData() (pyrosetta.rosetta.protocols.sparta.GDB method) (pyrosetta.rosetta.RDKit.Dict method) getDegree() (pyrosetta.rosetta.RDKit.Atom method) getDensityMap() (in module pyrosetta.rosetta.core.scoring.electron_density) getDensityMap_legacy() (in module pyrosetta.rosetta.core.scoring.electron_density) getDict() (pyrosetta.rosetta.RDKit.Atom method) (pyrosetta.rosetta.RDKit.Bond method) (pyrosetta.rosetta.RDKit.Conformer method) (pyrosetta.rosetta.RDKit.RDProps method) (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) getDiff() (in module pyrosetta.rosetta.protocols.sparta) getDihedralAngle() (pyrosetta.rosetta.protocols.sparta.PDB method) getDist() (pyrosetta.rosetta.protocols.sparta.PDB method) GetDots() (pyrosetta.rosetta.core.scoring.sc.ContactMolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeSimilarityCalculator method) getEffectiveBfactor() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) getEndAtom() (pyrosetta.rosetta.RDKit.Bond method) getEndAtomIdx() (pyrosetta.rosetta.RDKit.Bond method) getEntry() (pyrosetta.rosetta.protocols.sparta.PDB method) getEntryCount() (pyrosetta.rosetta.protocols.sparta.GDB method) GetExemplarNumAtoms() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) GetExemplarNumClusters() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) GetExemplarNumPolarAtoms() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) getExplicitValence() (pyrosetta.rosetta.RDKit.Atom method) getFiberDiffractionData() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) getFiberDiffractionData_legacy() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) getField() (pyrosetta.rosetta.protocols.sparta.PDB method) getFormalCharge() (pyrosetta.rosetta.RDKit.Atom method) getFSC() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) getGrid() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) gethash() (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) getHBondDist() (pyrosetta.rosetta.protocols.sparta.PDB method) getHybridization() (pyrosetta.rosetta.RDKit.Atom method) getId() (pyrosetta.rosetta.RDKit.Conformer method) getIdx() (pyrosetta.rosetta.RDKit.Atom method) (pyrosetta.rosetta.RDKit.Bond method) getImplicitValence() (pyrosetta.rosetta.RDKit.Atom method) getInfoLine() (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) getIntensities() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) getIsAromatic() (pyrosetta.rosetta.RDKit.Atom method) (pyrosetta.rosetta.RDKit.Bond method) getIsConjugated() (pyrosetta.rosetta.RDKit.Bond method) getIsotope() (pyrosetta.rosetta.RDKit.Atom method) getK() (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) getLargestClusterSize() (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) getLastAtom() (pyrosetta.rosetta.RDKit.RWMol method) getline() (in module pyrosetta.rosetta.ObjexxFCL) (in module pyrosetta.rosetta.utility.io) (pyrosetta.rosetta.std.ifstream method) (pyrosetta.rosetta.std.iostream method) (pyrosetta.rosetta.std.istream method) (pyrosetta.rosetta.std.istringstream method) (pyrosetta.rosetta.std.stringstream method) (pyrosetta.rosetta.std.wistream method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) getListNames() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) getloc() (pyrosetta.rosetta.std.filebuf method) (pyrosetta.rosetta.std.ios_base method) (pyrosetta.rosetta.std.streambuf method) (pyrosetta.rosetta.std.stringbuf method) (pyrosetta.rosetta.std.wstreambuf method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_streambuf_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) getLoopsToBuildFromBlueprint() (pyrosetta.rosetta.protocols.forge.remodel.RemodelData method) getLoopsToBuildFromFile() (pyrosetta.rosetta.protocols.forge.remodel.RemodelData method) getMapSpacingAndOrigin() (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) getMass() (pyrosetta.rosetta.RDKit.Atom method) getMatrixPointer() (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t method) getMax() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) GetMaximumElectrons() (pyrosetta.rosetta.core.chemical.Bond method) getMaxValue() (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) getMean() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) getMin() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) GetMinimumElectrons() (pyrosetta.rosetta.core.chemical.Bond method) getMinValue() (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) getMLweight() (in module pyrosetta.rosetta.core.util) getMLweight_cart() (in module pyrosetta.rosetta.core.util) GetMostStableType() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) getName() (pyrosetta.rosetta.utility.tag.Tag method) getNeighbors() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) getNetClusterSize() (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) getNextRCadj() (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib method) getNoImplicit() (pyrosetta.rosetta.RDKit.Atom method) getNonPODStatus() (pyrosetta.rosetta.RDKit.Dict method) getNumAtoms() (pyrosetta.rosetta.RDKit.Conformer method) (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) getNumberMissCS() (pyrosetta.rosetta.protocols.sparta.ANN method) GetNumberOfElectrons() (pyrosetta.rosetta.core.chemical.Bond method) getNumberOfPoints() (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) GetNumberPossibleTypes() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) getNumBonds() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) getNumConformers() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) getNumExplicitHs() (pyrosetta.rosetta.RDKit.Atom method) getNumHeavyAtoms() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) getNumImplicitHs() (pyrosetta.rosetta.RDKit.Atom method) getNumRadicalElectrons() (pyrosetta.rosetta.RDKit.Atom method) getNumStatesPerAAPerBB() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) getOmega() (pyrosetta.rosetta.protocols.sparta.PDB method) getOneAAName() (pyrosetta.rosetta.protocols.sparta.PDB method) getOption() (pyrosetta.rosetta.utility.tag.Tag method) getOptions() (pyrosetta.rosetta.utility.tag.Tag method) getOrbitalShift() (pyrosetta.rosetta.protocols.sparta.PDB method) getOrigin() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) getOtherAtom() (pyrosetta.rosetta.RDKit.Bond method) getOtherAtomIdx() (pyrosetta.rosetta.RDKit.Bond method) getOwningMol() (pyrosetta.rosetta.RDKit.Atom method) (pyrosetta.rosetta.RDKit.Bond method) (pyrosetta.rosetta.RDKit.Conformer method) getParent() (pyrosetta.rosetta.utility.tag.Tag method) getPdbCodes() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) getPdbNames() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) getPDBs() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) getPerpendicular() (pyrosetta.rosetta.RDGeom.Point3D method) getPerturbationOrder() (pyrosetta.rosetta.RDKit.Atom method) getPhaseError() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) getPhenixInterface() (in module pyrosetta.rosetta.core.scoring.cryst) getPhi() (pyrosetta.rosetta.protocols.sparta.PDB method) getPose() (pyrosetta.rosetta.core.pose.signals.ConformationEvent method) (pyrosetta.rosetta.core.pose.signals.EnergyEvent method) (pyrosetta.rosetta.core.pose.signals.GeneralEvent method) getPoseExtraFloatScores() (in module pyrosetta.rosetta.core.pose) getPoseExtraScore() (in module pyrosetta.rosetta.core.pose) getPoseExtraStringScores() (in module pyrosetta.rosetta.core.pose) getPositions() (pyrosetta.rosetta.RDKit.Conformer method) getPrevRCadj() (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib method) GetPropertyName() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData static method) getPropIfPresent() (pyrosetta.rosetta.RDKit.Atom method) (pyrosetta.rosetta.RDKit.Bond method) (pyrosetta.rosetta.RDKit.Conformer method) (pyrosetta.rosetta.RDKit.RDProps method) (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) getPropList() (pyrosetta.rosetta.RDKit.Atom method) (pyrosetta.rosetta.RDKit.Bond method) (pyrosetta.rosetta.RDKit.Conformer method) (pyrosetta.rosetta.RDKit.RDProps method) (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) getPsi() (pyrosetta.rosetta.protocols.sparta.PDB method) getR() (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) getRandom() (pyrosetta.rosetta.numeric.random.mt19937_RG method) (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) getRandomDecoyNames() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) GetRBDOFValues (class in pyrosetta.rosetta.protocols.matdes) GetRBDOFValuesCreator (class in pyrosetta.rosetta.protocols.matdes) getRC() (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib method) getRCadj() (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib method) getRelaxResidues() (pyrosetta.rosetta.protocols.pockets.EggshellGrid static method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid static method) (pyrosetta.rosetta.protocols.pockets.PocketGrid static method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid static method) getResidName() (pyrosetta.rosetta.protocols.sparta.GDB method) getResidueRange() (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) getResInfo() (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib method) getResolution() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) getResolutionBins() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) GetResults() (pyrosetta.rosetta.core.scoring.sc.ContactMolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ElectrostaticComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ElectrostaticSimilarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeSimilarityCalculator method) getRfree() (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) getRingInfo() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) getRMS() (in module pyrosetta.rosetta.protocols.sparta) getRSCC() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) getRT() (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) getScore() (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) getScoreAndDerivs() (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) getScoreWindowContext() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) getSCscaling() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) GetSDAltFileID() (pyrosetta.rosetta.core.chemical.Bond method) GetSDFileID() (pyrosetta.rosetta.core.chemical.Bond method) getSecStruct() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) getSeed() (pyrosetta.rosetta.numeric.random.mt19937_RG method) (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) getSigAxisR() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) getSigAxisT() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) getSigOffAxisR() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) getSigOffAxisT() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) getSimPDB() (pyrosetta.rosetta.protocols.cluster.calibur.PreloadedPDB method) getSlashChar() (pyrosetta.rosetta.protocols.sparta.ANN method) getSolutionSet() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) getSTD() (in module pyrosetta.rosetta.protocols.sparta) getStdev() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) getStereo() (pyrosetta.rosetta.RDKit.Bond method) getStereoAtoms() (pyrosetta.rosetta.RDKit.Bond method) getStubByName() (pyrosetta.rosetta.protocols.hotspot_hashing.StubGenerator static method) getSymbol() (pyrosetta.rosetta.RDKit.Atom method) getsymmOps() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) getTag() (pyrosetta.rosetta.RDKit.RDValue method) (pyrosetta.rosetta.utility.tag.Tag method) getTags() (pyrosetta.rosetta.utility.tag.Tag method) getThreeAAName() (pyrosetta.rosetta.protocols.sparta.PDB method) getThresholdAndDecoys() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) GetTime() (pyrosetta.rosetta.basic.gpu.Timer method) getTop() (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) getTotalDegree() (pyrosetta.rosetta.RDKit.Atom method) getTotalMemoryUsage() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintGraph method) (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.jd3.JobDigraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t method) getTotalNumHs() (pyrosetta.rosetta.RDKit.Atom method) getTotalValence() (pyrosetta.rosetta.RDKit.Atom method) getTransform() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) GetTrimmedDots() (pyrosetta.rosetta.core.scoring.sc.ContactMolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeSimilarityCalculator method) getUniqueAtomWithBookmark() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) getUniqueBondWithBookmark() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) getVal() (pyrosetta.rosetta.RDKit.Dict method) getValenceContrib() (pyrosetta.rosetta.RDKit.Bond method) getValIfPresent() (pyrosetta.rosetta.RDKit.Dict method) getValue() (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) getValues() (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) getWeight() (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib method) getWindow() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) getxform() (in module pyrosetta.rosetta.core.fragment) (in module pyrosetta.rosetta.protocols.sic_dock) GHOST_COLOR (pyrosetta.rosetta.protocols.viewer.graphics_states_param.ColorMode attribute) ghost_loops() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) give_dihedral_index() (in module pyrosetta.rosetta.protocols.ncbb) given_names() (pyrosetta.rosetta.basic.citation_manager.AuthorNames method) global() (pyrosetta.rosetta.std.locale static method) global2local() (pyrosetta.rosetta.core.kinematics.Stub method) global_auto_rescale() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) global_for_parameters_set (pyrosetta.rosetta.core.conformation.parametric.ParameterizationCalculatorProperties property) global_for_parameters_set() (pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.Parameter method) (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) global_job_id (pyrosetta.rosetta.protocols.jd3.dag_node_managers.ResultElements property) global_job_id() (pyrosetta.rosetta.protocols.jd3.JGJobNode method) global_loop_rmsd() (in module pyrosetta.rosetta.protocols.antibody) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) global_mapping() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) global_offset() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragSetCollection method) (pyrosetta.rosetta.core.fragment.MinimalFragSet method) (pyrosetta.rosetta.core.fragment.OrderedFragSet method) global_optimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) global_orientation_from_frame3() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) global_pos1() (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim method) global_pos2() (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim method) global_position() (pyrosetta.rosetta.protocols.topology_broker.claims.BBClaim method) global_rotamer_id() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) global_rotid_start_for_moltenres_in_bbconf() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) global_sample_res_list() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) global_sequence() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) GlobalResidueTypeSet (class in pyrosetta.rosetta.core.chemical) GLUTARYLATION (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes attribute) GLUTATHIONYLATION (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes attribute) gly_dG (pyrosetta.rosetta.protocols.analysis.InterfaceData property) glycam_pdb_format() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) glycan_tree_branch_sequence() (pyrosetta.rosetta.core.pose.Pose method) GLYCAN_TREE_OBSERVER (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType attribute) glycan_tree_sequence() (pyrosetta.rosetta.core.pose.Pose method) glycan_tree_set() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) GlycanDockProtocol (class in pyrosetta.rosetta.protocols.glycan_docking) GlycanDockProtocolCreator (class in pyrosetta.rosetta.protocols.glycan_docking) GlycanInfoMover (class in pyrosetta.rosetta.protocols.analysis) GlycanInfoMoverCreator (class in pyrosetta.rosetta.protocols.analysis) GlycanLayerSelector (class in pyrosetta.rosetta.core.select.residue_selector) GlycanLayerSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) GlycanNode (class in pyrosetta.rosetta.core.conformation.carbohydrates) GlycanPositionSelector (class in pyrosetta.rosetta.core.select.residue_selector) GlycanPositionSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) GlycanResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) GlycanResidueSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) GlycanSampler (class in pyrosetta.rosetta.protocols.carbohydrates) GlycanSamplerCreator (class in pyrosetta.rosetta.protocols.carbohydrates) GlycanSequon (class in pyrosetta.rosetta.protocols.carbohydrates) GlycanSequonsSelector (class in pyrosetta.rosetta.core.select.residue_selector) GlycanSequonsSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) GlycanTree (class in pyrosetta.rosetta.core.conformation.carbohydrates) GlycanTreeMinMover (class in pyrosetta.rosetta.protocols.carbohydrates) GlycanTreeMinMoverCreator (class in pyrosetta.rosetta.protocols.carbohydrates) GlycanTreeModeler (class in pyrosetta.rosetta.protocols.carbohydrates) GlycanTreeModelerCreator (class in pyrosetta.rosetta.protocols.carbohydrates) GlycanTreeSet (class in pyrosetta.rosetta.core.conformation.carbohydrates) GlycanTreeSetObserver (class in pyrosetta.rosetta.core.conformation.carbohydrates) GLYCOLYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) GlycopeptideDockingFlags (class in pyrosetta.rosetta.protocols.glycopeptide_docking) GlycopeptideDockingHighResRefinement (class in pyrosetta.rosetta.protocols.glycopeptide_docking) GlycopeptideDockingLowResRefinement (class in pyrosetta.rosetta.protocols.glycopeptide_docking) GlycopeptideDockingProtocol (class in pyrosetta.rosetta.protocols.glycopeptide_docking) GlycopeptideDockingProtocolCreator (class in pyrosetta.rosetta.protocols.glycopeptide_docking) GLYCOSIDE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) glycosylate_pose() (in module pyrosetta.rosetta.core.pose.carbohydrates) glycosylate_pose_by_file() (in module pyrosetta.rosetta.core.pose.carbohydrates) glycosylate_residues() (in module pyrosetta.rosetta.protocols.glycopeptide_docking) glycosylation_residue_substrate() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) GlycosyltransferaseMover (class in pyrosetta.rosetta.protocols.enzymatic_movers) GlycosyltransferaseMoverCreator (class in pyrosetta.rosetta.protocols.enzymatic_movers) gm (pyrosetta.rosetta.protocols.tcr.TCRmodel.tcrtmplts property) (pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs property) gmax_cutoff_for_convergence() (pyrosetta.rosetta.core.optimization.MinimizerOptions method) GNRA_TETRALOOP (pyrosetta.rosetta.core.scoring.rna.RNA_MotifType attribute) go() (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringProtocol method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.BOINCJobDistributor method) (pyrosetta.rosetta.protocols.jd2.FileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.JobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.ShuffleFileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.VectorPoseJobDistributor method) (pyrosetta.rosetta.protocols.jd3.job_distributors.VanillaJobDistributor method) (pyrosetta.rosetta.protocols.jd3.JobDistributor method) (pyrosetta.rosetta.protocols.loophash.MPI_LoopHashRefine method) (pyrosetta.rosetta.protocols.loophash.MPI_LoopHashRefine_Emperor method) (pyrosetta.rosetta.protocols.loophash.MPI_LoopHashRefine_Master method) (pyrosetta.rosetta.protocols.mpi_refinement.MPI_Refine_Emperor method) (pyrosetta.rosetta.protocols.mpi_refinement.MPI_Refine_Master method) (pyrosetta.rosetta.protocols.mpi_refinement.MPI_Refinement method) (pyrosetta.rosetta.protocols.optimize_weights.IterativeOptEDriver method) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.wum.MPI_WorkUnitManager method) (pyrosetta.rosetta.protocols.wum.MPI_WorkUnitManager_Slave method) (pyrosetta.rosetta.protocols.wum.WorkUnitManager method) go_mpi() (pyrosetta.rosetta.protocols.jd2.VectorPoseJobDistributor method) go_serial() (pyrosetta.rosetta.protocols.jd2.VectorPoseJobDistributor method) goap (pyrosetta.rosetta.core.scoring.ScoreType attribute) goap_angle (pyrosetta.rosetta.core.scoring.ScoreType attribute) goap_dist (pyrosetta.rosetta.core.scoring.ScoreType attribute) GoapEnergy (class in pyrosetta.rosetta.core.energy_methods) GoapEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) GoapRsdType (class in pyrosetta.rosetta.core.energy_methods) good (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor.CompletionMessage property) good() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) good_angle_count (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) good_atr_rotamer_count (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) good_bin_rep_count (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) good_distance_count (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) good_fix_pos_ (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer.CM_SuggestFixResidue property) good_rep_rotamer_count (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) grab_additional_pose_data() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) grab_main_chain_torsion_set_list() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) grab_pose_cache_data() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) grab_pose_energies_table() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) grab_simple_metric_data() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) GrabAllCollector (class in pyrosetta.rosetta.protocols.frag_picker) grad() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) gradient() (pyrosetta.rosetta.core.chemical.mainchain_potential.MainchainScoreTable method) gradnorm() (in module pyrosetta.rosetta.numeric.crick_equations) gradual_constraints() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) graft() (pyrosetta.rosetta.protocols.metal_interface.MatchGrafter method) graft_cdr() (in module pyrosetta.rosetta.protocols.tcr) graft_cdr_loops() (in module pyrosetta.rosetta.protocols.antibody.grafting) graft_cdr_to_fw() (in module pyrosetta.rosetta.protocols.tcr) graft_closed() (in module pyrosetta.rosetta.protocols.grafting) graft_framework() (in module pyrosetta.rosetta.protocols.tcr) graft_is_closed() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) graft_loop() (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) GraftCDRLoopsProtocol (class in pyrosetta.rosetta.protocols.antibody) GraftedStemOptimizer (class in pyrosetta.rosetta.protocols.antibody) Grafting_Base_Exception (class in pyrosetta.rosetta.protocols.antibody.grafting) GraftMover (class in pyrosetta.rosetta.protocols.antibody_legacy) GraftMoverBase (class in pyrosetta.rosetta.protocols.grafting) GraftOneCDRLoop (class in pyrosetta.rosetta.protocols.antibody) GraftOneMover (class in pyrosetta.rosetta.protocols.antibody_legacy) GraftSwitchMover (class in pyrosetta.rosetta.protocols.switches) GraftSwitchMoverCreator (class in pyrosetta.rosetta.protocols.switches) grandparent (pyrosetta.rosetta.core.kinematics.inverse.InternalCoordAtoms property) Graph (class in pyrosetta.rosetta.utility.graph) graph() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphContainer method) GraphicsState (class in pyrosetta.rosetta.protocols.viewer) GreaterThanConstraint (class in pyrosetta.rosetta.basic.database.schema_generator) greedy_around() (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) GreedyKCenter (class in pyrosetta.rosetta.protocols.toolbox) GreedyOptMutationMover (class in pyrosetta.rosetta.protocols.design_opt) GreedyOptMutationMoverCreator (class in pyrosetta.rosetta.protocols.design_opt) greek_distance() (pyrosetta.rosetta.core.chemical.Atom method) GreekDistance (class in pyrosetta.rosetta.core.chemical) Green (pyrosetta.rosetta.utility.CSI.CSI_Enum attribute) GreenPacker (class in pyrosetta.rosetta.protocols.minimization_packing) grid() (pyrosetta.rosetta.protocols.match.BumpGrid method) (pyrosetta.rosetta.protocols.match.downstream.ActiveSiteGrid method) grid_atoms() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) grid_centering_mode (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) grid_data (pyrosetta.rosetta.core.scoring.APBSResult property) grid_name() (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid static method) grid_rotamer_trials() (in module pyrosetta.rosetta.protocols.ligand_docking) grid_rotamer_trials_atr_rep() (in module pyrosetta.rosetta.protocols.ligand_docking) grid_score() (in module pyrosetta.rosetta.protocols.ligand_docking) grid_score_atr_rep() (in module pyrosetta.rosetta.protocols.ligand_docking) grid_scores() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) grid_set_prototype() (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) grid_size() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_double_t method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_float method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_float_t method) (pyrosetta.rosetta.protocols.sic_dock.xyzStripeHashPoseWithMeta method) grid_size2() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) grid_to_kin() (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid method) grid_vdw (pyrosetta.rosetta.core.scoring.ScoreType attribute) grid_vdw_weight() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) GridBase (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) GridCreator (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) GriddedAtomTreeMultifunc (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) GridFactory (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbAcc_t (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbDon_t (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) GridInfo (class in pyrosetta.rosetta.core.energy_methods) gridlig_active_site_definition() (pyrosetta.rosetta.protocols.match.MatcherTask method) gridlig_file_name() (pyrosetta.rosetta.protocols.match.MatcherTask method) GridManager (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) gridpt() (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) GridScorer (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) GridSearchIterator (class in pyrosetta.rosetta.protocols.scoring.methods.pcs) GridSearchIterator_Ts1 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) GridSearchIterator_Ts2 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) GridSearchIterator_Ts3 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) GridSearchIterator_Ts4 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) GridSearchIteratorCA (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) GridSet (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) gridStep_ (pyrosetta.rosetta.protocols.electron_density.SelectDensityPointsOptions property) group() (pyrosetta.rosetta.core.conformation.ResidueKinWriter method) (pyrosetta.rosetta.protocols.match.output.ResidueKinemageWriter method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage method) group1_resstring() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) group1_selector() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) group1_set() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) group2_resstring() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) group2_selector() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) group2_set() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) group_atom_index (pyrosetta.rosetta.core.io.mmtf.sd_index property) group_heavyatom_index_to_group_index() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) group_id() (pyrosetta.rosetta.protocols.minimization_packing.ChainGroupDiscriminator method) (pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator method) (pyrosetta.rosetta.protocols.minimization_packing.UserDefinedGroupDiscriminator method) group_index (pyrosetta.rosetta.core.io.mmtf.sd_index property) group_name() (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) group_size() (pyrosetta.rosetta.protocols.cluster.Cluster method) group_size_ (pyrosetta.rosetta.protocols.cluster.Cluster property) GroupDiscriminator (class in pyrosetta.rosetta.protocols.minimization_packing) GroupElec (class in pyrosetta.rosetta.core.scoring.elec) grouper_ds_rmsd() (pyrosetta.rosetta.protocols.match.MatcherTask method) grouper_name() (pyrosetta.rosetta.protocols.match.MatcherTask method) groups() (pyrosetta.rosetta.protocols.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) grow() (in module pyrosetta.rosetta.protocols.ligand_docking) grow_all_loops() (pyrosetta.rosetta.protocols.loops.Loops method) grow_loop() (pyrosetta.rosetta.protocols.loops.Loops method) grow_loop_away_from_sheets() (pyrosetta.rosetta.protocols.loops.Loops method) GrowLeft (class in pyrosetta.rosetta.protocols.forge.build) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBInstructionType attribute) GrowLigand (class in pyrosetta.rosetta.protocols.ligand_docking) GrowLigandCreator (class in pyrosetta.rosetta.protocols.ligand_docking) GrowPeptides (class in pyrosetta.rosetta.protocols.seeded_abinitio) GrowPeptidesCreator (class in pyrosetta.rosetta.protocols.seeded_abinitio) GrowPeptidesSegment (class in pyrosetta.rosetta.protocols.seeded_abinitio) GrowRight (class in pyrosetta.rosetta.protocols.forge.build) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBInstructionType attribute) grp_cpfxn() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) grpelec_context_dependent() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) grpelec_fade_hbond() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) grpelec_fade_param1() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) grpelec_fade_param2() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) grpelec_fade_type() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) gt (pyrosetta.rosetta.protocols.simple_filters.comparison_type attribute) GT_Expression (class in pyrosetta.rosetta.numeric.expression_parser) gt_or_eq (pyrosetta.rosetta.protocols.simple_filters.comparison_type attribute) GTE_Expression (class in pyrosetta.rosetta.numeric.expression_parser) gtol (pyrosetta.rosetta.numeric.nls.lm_control_struct property) guarantee_no_DNA() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) GuardedLoopsFromFile (class in pyrosetta.rosetta.protocols.loops) guess_rbsegs_from_pose() (in module pyrosetta.rosetta.protocols.rbsegment_relax) GunnCost (class in pyrosetta.rosetta.protocols.frag_picker.scores) (class in pyrosetta.rosetta.protocols.simple_moves) GunnCostScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) GunnTuple (class in pyrosetta.rosetta.protocols.frag_picker.scores) (class in pyrosetta.rosetta.protocols.simple_moves) gunzip() (in module pyrosetta.rosetta.utility.file) gzip() (in module pyrosetta.rosetta.core.io.silent) (in module pyrosetta.rosetta.utility.file) gzipped() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method)