Index – K

K (pyrosetta.rosetta.core.chemical.element.Elements attribute) k (pyrosetta.rosetta.core.scoring.TorsionParams property) (pyrosetta.rosetta.protocols.cluster.Exemplar property) (pyrosetta.rosetta.protocols.md.Constraint property) (pyrosetta.rosetta.protocols.normalmode.ContactStruct property) k() (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.GenTorsionParams method) K() (pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.methods.BBIndepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.methods.CartBondedParameters method) k() (pyrosetta.rosetta.core.scoring.SpringParams method) k1 (pyrosetta.rosetta.core.scoring.fiber_diffraction.Hankel property) k2 (pyrosetta.rosetta.core.scoring.fiber_diffraction.Hankel property) k6() (pyrosetta.rosetta.core.scoring.GenTorsionParams method) k_angle() (pyrosetta.rosetta.core.energy_methods.IdealParametersDatabase method) k_length() (pyrosetta.rosetta.core.energy_methods.IdealParametersDatabase method) k_medoids_on_the_fly() (in module pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster) k_medoids_with_edge_precalculation() (in module pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster) k_torsion() (pyrosetta.rosetta.core.energy_methods.IdealParametersDatabase method) k_torsion_improper() (pyrosetta.rosetta.core.energy_methods.IdealParametersDatabase method) k_torsion_proton() (pyrosetta.rosetta.core.energy_methods.IdealParametersDatabase method) Kabat (pyrosetta.rosetta.protocols.antibody.CDRDefinitionEnum attribute) Kabat_Scheme (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingSchemeEnum attribute) Kabsch() (pyrosetta.rosetta.protocols.hybridization.TMalign method) kappa (pyrosetta.rosetta.protocols.antibody.LightChainTypeEnum attribute) Kappa() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) KAPPA_ATOM (pyrosetta.rosetta.core.chemical.GreekDistance attribute) KarplusFunc (class in pyrosetta.rosetta.core.scoring.func) kbt() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) KCluster (class in pyrosetta.rosetta.protocols.toolbox) KClusterData (class in pyrosetta.rosetta.protocols.toolbox) KClusterElement (class in pyrosetta.rosetta.protocols.toolbox) KDNode (class in pyrosetta.rosetta.numeric.kdtree) KDPoint (class in pyrosetta.rosetta.numeric.kdtree) KDPoint_MinDist (class in pyrosetta.rosetta.numeric.kdtree) KDPointList (class in pyrosetta.rosetta.numeric.kdtree) KDTree (class in pyrosetta.rosetta.numeric.kdtree) KDTREE_CONSTRUCT (pyrosetta.rosetta.basic.ProfTag attribute) KDTREE_SEARCH (pyrosetta.rosetta.basic.ProfTag attribute) keep_1st_child_pos() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) keep_aas() (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAAS method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) keep_all_protocol() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) keep_bb (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBInstruction property) keep_center (pyrosetta.rosetta.protocols.toolbox.ClusterOptions property) keep_checkpoint_file() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) keep_dof_fixed() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) KEEP_EXISTING_BASE_TYPE (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) KEEP_EXISTING_DISULFIDES (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) KEEP_EXISTING_NONTERMINAL_VARIANT_TYPES_AND_DISALLLOW_INCOMPATIBLE_BASE_TYPES (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) KEEP_EXISTING_NONTERMINAL_VARIANT_TYPES_FOR_EXISTING_BASE_TYPE (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) KEEP_EXISTING_TERMINAL_VARIANT_TYPES_AT_POSITIONS (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) keep_filters() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) keep_fragments() (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) keep_history() (pyrosetta.rosetta.protocols.moves.PyMOLMover method) keep_hydro (pyrosetta.rosetta.core.chemical.rdkit.RestypeToRDMolOptions property) KEEP_IN_MEMORY (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum attribute) keep_input_protonation_state() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) keep_input_scores() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) keep_known_bb_torsions_at_junctions() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) keep_motif() (pyrosetta.rosetta.protocols.motifs.BuildPosition method) keep_motifhit() (pyrosetta.rosetta.protocols.motifs.BuildPosition method) keep_native() (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation method) KEEP_ROTAMER (pyrosetta.rosetta.core.pack.rotamer_set.BumpSelectorDecision attribute) keep_rotamer() (pyrosetta.rosetta.protocols.motifs.BuildPosition method) keep_rotamer_assignment_for_last_entity (pyrosetta.rosetta.protocols.pack_daemon.DaemonSetMessage attribute) keep_sequence_symmetry() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) keep_stats_type() (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) keep_stub_in_residue() (pyrosetta.rosetta.core.kinematics.Edge method) keep_top_pose() (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) keep_trying() (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) KeepLigandContactsRequirement (class in pyrosetta.rosetta.protocols.sewing.requirements) KeepLigandContactsRequirementCreator (class in pyrosetta.rosetta.protocols.sewing.requirements) KeepRegionMover (class in pyrosetta.rosetta.protocols.grafting.simple_movers) KeepRegionMoverCreator (class in pyrosetta.rosetta.protocols.grafting.simple_movers) KeepSequenceSymmetry (class in pyrosetta.rosetta.core.pack.task.operation) KeepSequenceSymmetryCreator (class in pyrosetta.rosetta.core.pack.task.operation) kept_match() (pyrosetta.rosetta.protocols.match.output.BestMatchesCollection method) kept_match_dspos1() (pyrosetta.rosetta.protocols.match.output.BestMatchesCollection method) Keq() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_PNearToArbitraryStateSummary method) kernel_mult() (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTraceFactory method) KETOSE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) Key (class in pyrosetta.rosetta.utility.keys) key (pyrosetta.rosetta.protocols.loophash.LeapIndex property) (pyrosetta.rosetta.RDKit.Dict.Pair property) key() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.pose_metric_calculators.MetricValueGetter method) (pyrosetta.rosetta.utility.keys.KeyLookup_utility_options_OptionKey_t static method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) key1() (pyrosetta.rosetta.utility.keys.Key2Tuple_double_double_t method) (pyrosetta.rosetta.utility.keys.Key2Tuple_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.keys.Key3Tuple_protocols_loops_Loop_std_shared_ptr_core_kinematics_MoveMap_std_shared_ptr_core_kinematics_MoveMap_t method) (pyrosetta.rosetta.utility.keys.Key3Tuple_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.keys.Key4Tuple_unsigned_long_unsigned_long_unsigned_long_unsigned_long_t method) key2() (pyrosetta.rosetta.utility.keys.Key2Tuple_double_double_t method) (pyrosetta.rosetta.utility.keys.Key2Tuple_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.keys.Key3Tuple_protocols_loops_Loop_std_shared_ptr_core_kinematics_MoveMap_std_shared_ptr_core_kinematics_MoveMap_t method) (pyrosetta.rosetta.utility.keys.Key3Tuple_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.keys.Key4Tuple_unsigned_long_unsigned_long_unsigned_long_unsigned_long_t method) Key2Tuple_double_double_t (class in pyrosetta.rosetta.utility.keys) Key2Tuple_unsigned_long_unsigned_long_t (class in pyrosetta.rosetta.utility.keys)

key3() (pyrosetta.rosetta.utility.keys.Key3Tuple_protocols_loops_Loop_std_shared_ptr_core_kinematics_MoveMap_std_shared_ptr_core_kinematics_MoveMap_t method) (pyrosetta.rosetta.utility.keys.Key3Tuple_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.keys.Key4Tuple_unsigned_long_unsigned_long_unsigned_long_unsigned_long_t method) Key3Tuple_protocols_loops_Loop_std_shared_ptr_core_kinematics_MoveMap_std_shared_ptr_core_kinematics_MoveMap_t (class in pyrosetta.rosetta.utility.keys) Key3Tuple_unsigned_long_unsigned_long_unsigned_long_t (class in pyrosetta.rosetta.utility.keys) key4() (pyrosetta.rosetta.utility.keys.Key4Tuple_unsigned_long_unsigned_long_unsigned_long_unsigned_long_t method) Key4Tuple_unsigned_long_unsigned_long_unsigned_long_unsigned_long_t (class in pyrosetta.rosetta.utility.keys) key_comp() (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairSet 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) key_eq() (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) key_set_ (pyrosetta.rosetta.core.scoring.motif.MotifHash property) KeyError (class in pyrosetta.rosetta.utility.excn) KeyLookup_utility_options_OptionKey_t (class in pyrosetta.rosetta.utility.keys) keyname() (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator method) (pyrosetta.rosetta.core.chemical.PatchOperationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.SilentStructCreator method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibraryCreator method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibraryCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetricCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetricCreator method) (pyrosetta.rosetta.core.pack.palette.CustomBaseTypePackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.DefaultPackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.NCAADefaultPackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.NoDesignPackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.PackerPaletteCreator method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibraryCreator method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibraryCreator method) (pyrosetta.rosetta.core.pack.rotamers.SingleNCAARotamerLibraryCreator method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryCreator method) (pyrosetta.rosetta.core.pack.rotamers.StoredRotamerLibraryCreator method) (pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLT static method) (pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.AllResFilter static method) (pyrosetta.rosetta.core.pack.task.operation.AllResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.AnyResFilter static method) (pyrosetta.rosetta.core.pack.task.operation.AnyResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet static method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSetCreator method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer static method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerCreator method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet static method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSetCreator method) (pyrosetta.rosetta.core.pack.task.operation.ChainIs static method) (pyrosetta.rosetta.core.pack.task.operation.ChainIsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ChainIsnt static method) (pyrosetta.rosetta.core.pack.task.operation.ChainIsntCreator method) (pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShell static method) (pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShellCreator method) (pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions static method) (pyrosetta.rosetta.core.pack.task.operation.DesignRestrictionsCreator method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative static method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeCreator method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLT static method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer static method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealerCreator method) (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer static method) (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealerCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff static method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLT static method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers static method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric static method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT static method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation static method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrent static method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentCreator method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLT static method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandline static method) (pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandlineCreator method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandline static method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandlineCreator method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection static method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollectionCreator method) (pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry static method) (pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetryCreator method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides static method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfidesCreator method) (pyrosetta.rosetta.core.pack.task.operation.NoResFilter static method) (pyrosetta.rosetta.core.pack.task.operation.NoResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues static method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResiduesCreator method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset static method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubsetCreator method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG static method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHGCreator method) (pyrosetta.rosetta.core.pack.task.operation.OptH static method) (pyrosetta.rosetta.core.pack.task.operation.OptHCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBeta static method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLT static method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking static method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepackingCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLT static method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties static method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitResiduePropertiesCreator method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes static method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypesCreator method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfile static method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents static method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEventsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty static method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasPropertyCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIs static method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsnt static method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsntCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueLacksProperty static method) (pyrosetta.rosetta.core.pack.task.operation.ResidueLacksPropertyCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3Is static method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3IsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3Isnt static method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3IsntCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIs static method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsnt static method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsntCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoHasLabel static method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoHasLabelCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoLacksLabel static method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoLacksLabelCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueTypeFilter static method) (pyrosetta.rosetta.core.pack.task.operation.ResidueTypeFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAAS static method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASExceptNativeRLT static method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASExceptNativeRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASRLT static method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictInteractionGraphThreadsOperation static method) (pyrosetta.rosetta.core.pack.task.operation.RestrictInteractionGraphThreadsOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking static method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepackingCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepacking static method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepackingCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepackingRLT static method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepackingRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToResidueProperties static method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToResiduePropertiesCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToSpecifiedBaseResidueTypes static method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToSpecifiedBaseResidueTypesCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign static method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesignCreator method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion static method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosionCreator method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerCouplings static method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerCouplingsCreator method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerLinks static method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerLinksCreator method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.UseMultiCoolAnnealer static method) (pyrosetta.rosetta.core.pack.task.operation.UseMultiCoolAnnealerCreator method) (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelectorCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NamedAtomPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.ExclusivelySharedJumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.JumpForResidueCreator method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.JumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.BFactorSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.BinSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.BlockSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ChainSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ConfluentSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.FractionSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelectorCreator method) (pyrosetta.rosetta.core.sequence.ChemicalShiftSequenceCreator method) (pyrosetta.rosetta.core.sequence.CompositeSequenceCreator method) (pyrosetta.rosetta.core.sequence.SequenceCouplingCreator method) (pyrosetta.rosetta.core.sequence.SequenceCreator method) (pyrosetta.rosetta.core.sequence.SequenceProfileCreator method) (pyrosetta.rosetta.core.sequence.SimpleSequenceCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetricCreator method) (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMoverCreator method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMoverCreator method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMoverCreator method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCMCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMoverCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparerCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCMCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCMCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.JumpSampleDataCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCMCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCMCreator method) (pyrosetta.rosetta.protocols.abinitio.DomainAssemblyCreator method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetricCreator method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMoverCreator method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMoverCreator method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMoverCreator method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetricCreator method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMoverCreator method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetricCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafterCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMoverCreator method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMoverCreator method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMoverCreator method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMoverCreator method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMoverCreator method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForClusterCreator method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelectorCreator method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelectorCreator method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation static method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperationCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation static method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperationCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation static method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperationCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation static method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperationCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors static method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighborsCreator method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMoverCreator method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPreProCreator method) (pyrosetta.rosetta.protocols.backrub.BackrubMoverCreator method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocolCreator method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMoverCreator method) (pyrosetta.rosetta.protocols.buns.BuriedUnsatHbondFilter2Creator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.ConservedPosMutationFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoidsFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.OperatorFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2Creator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeightFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.SigmoidFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMoverCreator method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMoverCreator method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSamplerCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModelerCreator method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogensCreator method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMoverCreator method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMoverCreator method) (pyrosetta.rosetta.protocols.chemistries.ChemistryCreator method) (pyrosetta.rosetta.protocols.chemistries.ChemistryLoaderCreator method) (pyrosetta.rosetta.protocols.chemistries.PatchChemistryCreator method) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreCutoffFilterCreator method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilterCreator method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilterCreator method) (pyrosetta.rosetta.protocols.constraint_filters.ShowConstraintsFilterCreator method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraintsCreator method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraintsCreator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMoverCreator method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMoverCreator method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMoverCreator method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMoverCreator method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.contact_map.ContactMapCreator method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocolCreator method) (pyrosetta.rosetta.protocols.cryst.CrystRMSCreator method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMoverCreator method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMoverCreator method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMoverCreator method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMoverCreator method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMoverCreator method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMoverCreator method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMoverCreator method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMoverCreator method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMoverCreator method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMoverCreator method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfoCreator method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMoverCreator method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomainCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraintCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraintCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraintCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilterCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilterCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilterCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetricCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelectorCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlignCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutationsCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.MotifArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataCreator method) (pyrosetta.rosetta.protocols.denovo_design.constraints.FileConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilterCreator method) (pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilterCreator method) (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilterCreator method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilterCreator method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilterCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesignCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelectorCreator method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelectorCreator method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperationCreator method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMoverCreator method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNACreator method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMoverCreator method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesignCreator method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePackerCreator method) (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterface static method) (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterfaceCreator method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDnaCreator method) (pyrosetta.rosetta.protocols.dna.WatsonCrickRotamerCouplings static method) (pyrosetta.rosetta.protocols.dna.WatsonCrickRotamerCouplingsCreator method) (pyrosetta.rosetta.protocols.dna_dock.DNAClashCheckFilterCreator method) (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilterCreator method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMoverCreator method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacyCreator method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbationCreator method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocolCreator method) (pyrosetta.rosetta.protocols.docking.DockingProtocolCreator method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContactCreator method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocolCreator method) (pyrosetta.rosetta.protocols.docking.DockMinMoverCreator method) (pyrosetta.rosetta.protocols.docking.DockSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.docking.TemperedDockingCreator method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMoverCreator method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMoverCreator method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricCreator method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMoverCreator method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMoverCreator method) (pyrosetta.rosetta.protocols.electron_density.DensityZscoresCreator method) (pyrosetta.rosetta.protocols.electron_density.ReportFSCCreator method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensitiesCreator method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMoverCreator method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMoverCreator method) (pyrosetta.rosetta.protocols.environment.AutoCutDataCreator method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCMCreator method) (pyrosetta.rosetta.protocols.environment.EnvMoverCreator method) (pyrosetta.rosetta.protocols.environment.ScriptCMCreator method) (pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamers static method) (pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamersOperationCreator method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCstsCreator method) (pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfs static method) (pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfsCreator method) (pyrosetta.rosetta.protocols.enzdes.BackboneSamplerCreator method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface static method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterfaceOperationCreator method) (pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputterCreator method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputterCreator method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimizeCreator method) (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.LigBurialFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.LigDSasaFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.LigInterfaceEnergyFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedyCreator method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMoverCreator method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter static method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighterOperationCreator method) (pyrosetta.rosetta.protocols.enzdes.RemoveLigandFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.RepackWithoutLigandFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior static method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehaviorCreator method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMoverCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMoverCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetricCreator method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetricCreator method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCostFilterCreator method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinderFilterCreator method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserterFilterCreator method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMoverCreator method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutationCreator method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMoverCreator method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMoverCreator method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputterCreator method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputterCreator method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMoverCreator method) (pyrosetta.rosetta.protocols.features.ReportToDBCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDBCreator method) (pyrosetta.rosetta.protocols.filters.CalculatorFilterCreator method) (pyrosetta.rosetta.protocols.filters.CombinedFilterCreator method) (pyrosetta.rosetta.protocols.filters.CompoundFilterCreator method) (pyrosetta.rosetta.protocols.filters.ContingentFilterCreator method) (pyrosetta.rosetta.protocols.filters.FalseFilterCreator method) (pyrosetta.rosetta.protocols.filters.FilterCreator method) (pyrosetta.rosetta.protocols.filters.FilterValueMetricCreator method) (pyrosetta.rosetta.protocols.filters.IfThenFilterCreator method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilterCreator method) (pyrosetta.rosetta.protocols.filters.ReplicateFilterCreator method) (pyrosetta.rosetta.protocols.filters.StochasticFilterCreator method) (pyrosetta.rosetta.protocols.filters.TimeFilterCreator method) (pyrosetta.rosetta.protocols.filters.TrueFalseFilterCreator method) (pyrosetta.rosetta.protocols.filters.TrueFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDRCreator method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutationCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.CoreDunbrackFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.FragQualFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.InterlockingAromaFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.NcontactsFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.ParallelBetaPairingPreferenceFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureCountFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureHasResidueFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevelsCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMoverCreator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotentialCreator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergiesCreator method) (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocolCreator method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignCreator method) (pyrosetta.rosetta.protocols.flxbb.InterlockAromaCreator method) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation static method) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperationCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ConstraintFulfilmentFilterCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilterCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ScorePoseSegmentFromResidueSelectorFilterCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ConstraintResidueSelectorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.CutpointResidueSelectorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ProteinResidueSelectorCreator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersCstGeneratorCreator method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeCstGeneratorCreator method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCstsCreator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMoverCreator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinks static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinksCreator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityCstGeneratorCreator method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilterCreator method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKICCreator method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocolCreator method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocolCreator method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMoverCreator method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMoverCreator method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMoverCreator method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMoverCreator method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMoverCreator method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMoverCreator method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork static method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetworkCreator method) (pyrosetta.rosetta.protocols.hbnet.HBNetCreator method) (pyrosetta.rosetta.protocols.hbnet.HBNetScoreFilterCreator method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterfaceCreator method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelectorCreator method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerCreator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerCreator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterCreator method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixCreator method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleCreator method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelixCreator method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleCreator method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelixCreator method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbeCreator method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbationCreator method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSamplerCreator method) (pyrosetta.rosetta.protocols.hybridization.CartesianSamplerCreator method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocolCreator method) (pyrosetta.rosetta.protocols.idealize.IdealizeMoverCreator method) (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilterCreator method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMoverCreator method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMoverCreator method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.EmptyPoseJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.LazySilentFileJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.mmtfJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.ScreeningJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputterCreator method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.PDBChunkLibraryInputter static method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.PDBChunkLibraryInputterCreator method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputterCreator method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.PDBFullModelInputter static method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.PDBFullModelInputterCreator method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.SilentFileFullModelInputter static method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.SilentFileFullModelInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputter static method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputter static method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputter static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputterCreator method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMoverCreator method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragmentsCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFileCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFile static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFileCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogensCreator method) (pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslateCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDFCreator method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizerCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDockCreator method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigandCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDockerCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsembleCreator method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoaderCreator method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculatorCreator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoaderCreator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesignCreator method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackboneCreator method) (pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoaderCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsembleCreator method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformersCreator method) (pyrosetta.rosetta.protocols.ligand_docking.RotateCreator method) (pyrosetta.rosetta.protocols.ligand_docking.RotatesCreator method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogetherCreator method) (pyrosetta.rosetta.protocols.ligand_docking.StartFromCreator method) (pyrosetta.rosetta.protocols.ligand_docking.TransformCreator method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsembleCreator method) (pyrosetta.rosetta.protocols.ligand_docking.TranslateCreator method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFileCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapperCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtensionCreator method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModelerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilderCreator method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocolCreator method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefinerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefinerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefinerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSamplerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroidCreator method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatomCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifierCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapperCreator method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilterCreator method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoopsCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCMCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoaderCreator method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputterCreator method) (pyrosetta.rosetta.protocols.match.MatcherMoverCreator method) (pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperation static method) (pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperationCreator method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilterCreator method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMoverCreator method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValuesCreator method) (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilterCreator method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMoverCreator method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilterCreator method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMoverCreator method) (pyrosetta.rosetta.protocols.matdes.SymDofMoverCreator method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilterCreator method) (pyrosetta.rosetta.protocols.md.CartesianMDCreator method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraintCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraintCreator method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinderCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelixCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAnglesCreator method) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequenceCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibilityCreator method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSamplerCreator method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMoverCreator method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.MinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazyCreator method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMoverCreator method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMoverCreator method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealerCreator method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecoverCreator method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloResetCreator method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTestCreator method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMoverCreator method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftCreator method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPackerCreator method) (pyrosetta.rosetta.protocols.moves.DsspMoverCreator method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMoverCreator method) (pyrosetta.rosetta.protocols.moves.IfMoverCreator method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMoverCreator method) (pyrosetta.rosetta.protocols.moves.MoverCreator method) (pyrosetta.rosetta.protocols.moves.PyMOLMoverCreator method) (pyrosetta.rosetta.protocols.moves.RampingMoverCreator method) (pyrosetta.rosetta.protocols.moves.RandomMoverCreator method) (pyrosetta.rosetta.protocols.moves.SequenceMoverCreator method) (pyrosetta.rosetta.protocols.moves.SwitchMoverCreator method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricCreator method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetricCreator method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.SequenceMetricCreator method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocolCreator method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMoverCreator method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocolCreator method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMoverCreator method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinderCreator method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMoverCreator method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMoverCreator method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMoverCreator method) (pyrosetta.rosetta.protocols.nmr.pre.PREMoverCreator method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizerCreator method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMoverCreator method) (pyrosetta.rosetta.protocols.pack_interface.ProteinProteinInterfaceUpweighter static method) (pyrosetta.rosetta.protocols.pack_interface.ProteinProteinInterfaceUpweighterTaskOperationCreator method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DatabaseSessionLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator method) (pyrosetta.rosetta.protocols.parser.FragSetLoaderCreator method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoaderCreator method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoaderCreator method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoaderCreator method) (pyrosetta.rosetta.protocols.parser.PackerPaletteLoaderCreator method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoaderCreator method) (pyrosetta.rosetta.protocols.parser.ResLvlTaskOperationLoaderCreator method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoaderCreator method) (pyrosetta.rosetta.protocols.parser.SimpleMetricLoaderCreator method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoaderCreator method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotentialCreator method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequencesCreator method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilterCreator method) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMoverCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModelingCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMoverCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMoverCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMoverCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloserCreator method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporterCreator method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporterCreator method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporterCreator method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelectorCreator method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelectorCreator method) (pyrosetta.rosetta.protocols.pose_selectors.FilterCreator method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelectorCreator method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByPropertyCreator method) (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorerCreator method) (pyrosetta.rosetta.protocols.pose_sewing.filters.HasDisulfideFilterCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetricCreator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetricCreator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetricCreator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetricCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AtomicContactCountFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AverageDegreeFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.ClashWithTargetFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FNatFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.InterfaceHolesFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.IRmsdFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.LRmsdFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdSimpleFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SpecificResiduesNearInterfaceFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SSamountFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreLoopsFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.TorsionCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreakCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspotsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPoseCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbondsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechainsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycleCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycleCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinderCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChangeCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLineCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodelCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspotCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransformCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoopCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutationCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimizeCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechainsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTreeCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactorCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCstsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TryRotamersCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputterCreator method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMoverCreator method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetricCreator method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetricCreator method) (pyrosetta.rosetta.protocols.qsar.qsarCreator method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemageCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScoreCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoaderCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGridCreator method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoaderCreator method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetricCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMoverCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMoverCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMoverCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMoverCreator method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizerCreator method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMoverCreator method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequenceCreator method) (pyrosetta.rosetta.protocols.recon_design.FitnessFilterCreator method) (pyrosetta.rosetta.protocols.recon_design.MSDMoverCreator method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMoverCreator method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMoverCreator method) (pyrosetta.rosetta.protocols.relax.ClassicRelaxCreator method) (pyrosetta.rosetta.protocols.relax.FastRelaxCreator method) (pyrosetta.rosetta.protocols.relax.LocalRelaxCreator method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMoverCreator method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelaxCreator method) (pyrosetta.rosetta.protocols.residue_selectors.HBondSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.NativeSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMoverCreator method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelectorCreator method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMoverCreator method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMoverCreator method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMoverCreator method) (pyrosetta.rosetta.protocols.rigid.RollMoverCreator method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCMCreator method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMoverCreator method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMoverCreator method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocolCreator method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2ProtocolCreator method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMoverCreator method) (pyrosetta.rosetta.protocols.rna.movers.RNA_CoarsifyCreator method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DecoarsifyCreator method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMoverCreator method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMoverCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapperCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapperCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMoverCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocolCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMoverCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMoverCreator method) (pyrosetta.rosetta.protocols.score_filters.GeometryFilterCreator method) (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilterCreator method) (pyrosetta.rosetta.protocols.score_filters.ScoreTypeFilterCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGeneratorCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFoldCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCstCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoopsCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptidesCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTreeCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMoverCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizerCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegmentCreator method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMoverCreator method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMoverCreator method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.AssemblyRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.ClashRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.DsspSpecificLengthRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.KeepLigandContactsRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.LengthInResiduesRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandClashRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.NonTerminalStartingSegmentRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.SizeInSegmentsRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorerCreator method) (pyrosetta.rosetta.protocols.simple_ddg.AlaScanFilterCreator method) (pyrosetta.rosetta.protocols.simple_ddg.ddGCreator method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilterCreator method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScanCreator method) (pyrosetta.rosetta.protocols.simple_ddg.InterfaceBindingEnergyDensityFilterCreator method) (pyrosetta.rosetta.protocols.simple_ddg.SSElementBisectddGFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.AngleToVectorFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.AveragePathLengthFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreakFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.DisulfideEntropyFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.EnergyPerResidueFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ExpiryFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.FileExistFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.FileRemoveFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.HelixHelixAngleFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.HolesFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHydrophobicResidueContactsFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceSasaFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.InterRepeatContactFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.IntraRepeatContactFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.MembAccesResidueLipophilicityFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.MotifScoreFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.MPSpanAngleFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.NeighborTypeFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.NetChargeFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.NMerPSSMEnergyFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.NMerSVMEnergyFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.NonSequentialNeighborsFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.PackStatFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoseCommentFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.RangeFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ReadPoseExtraScoreFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.RepeatParameterFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ReportFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueBurialFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueChiralityFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDistanceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueIEFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueLipophilicityFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSelectionDistanceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSetChainEnergyFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResiduesInInterfaceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistanceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SidechainRmsdFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SpanTopologyMatchPoseFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SSElementLengthFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SSElementMotifContactFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinderFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.StemFinderFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareSASAFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TerminusDistanceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TMsAACompFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TMsSpanMembraneFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TotalSasaFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.Worst9merFilterCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairDataCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBinsCreator method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBinsCreator method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBondCreator method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdbCreator method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamersCreator method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfileCreator method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequenceCreator method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotifCreator method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopologyCreator method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidueCreator method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKACreator method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZCreator method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTreeCreator method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilitiesCreator method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsionCreator method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ShearMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SmallMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshotCreator method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.TumbleCreator method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPoseCreator method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMoverCreator method) (pyrosetta.rosetta.protocols.simple_task_operations.DockingNoRepack1 static method) (pyrosetta.rosetta.protocols.simple_task_operations.DockingNoRepack2 static method) (pyrosetta.rosetta.protocols.simple_task_operations.InterfaceTaskOperation static method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterface static method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterfaceCreator method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoops static method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors static method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighborsCreator method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsCreator method) (pyrosetta.rosetta.protocols.splice.AlignEndsMoverCreator method) (pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation static method) (pyrosetta.rosetta.protocols.splice.DesignInterfacesOperationCreator method) (pyrosetta.rosetta.protocols.splice.FindEndpointsOperation static method) (pyrosetta.rosetta.protocols.splice.FindEndpointsOperationCreator method) (pyrosetta.rosetta.protocols.splice.RBInMoverCreator method) (pyrosetta.rosetta.protocols.splice.RBOutMoverCreator method) (pyrosetta.rosetta.protocols.splice.RotLibOutCreator method) (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB static method) (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDBCreator method) (pyrosetta.rosetta.protocols.splice.SpliceCreator method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibodyCreator method) (pyrosetta.rosetta.protocols.splice.SpliceInCreator method) (pyrosetta.rosetta.protocols.splice.SpliceInTailCreator method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibodyCreator method) (pyrosetta.rosetta.protocols.splice.SpliceOutCreator method) (pyrosetta.rosetta.protocols.splice.SpliceOutTailCreator method) (pyrosetta.rosetta.protocols.splice.TailSegmentMoverCreator method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMoverCreator method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMoverCreator method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.FromScratchMoverCreator method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMoverCreator method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocolCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetryMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMoverCreator method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation static method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation static method) (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperation static method) (pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThread static method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThreadCreator method) (pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation static method) (pyrosetta.rosetta.protocols.task_operations.DesignAroundOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation static method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperation static method) (pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion static method) (pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosionCreator method) (pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation static method) (pyrosetta.rosetta.protocols.task_operations.JointSequenceOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation static method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2OperationCreator method) (pyrosetta.rosetta.protocols.task_operations.LinkResidues static method) (pyrosetta.rosetta.protocols.task_operations.LinkResiduesCreator method) (pyrosetta.rosetta.protocols.task_operations.ModifyAnnealer static method) (pyrosetta.rosetta.protocols.task_operations.ModifyAnnealerCreator method) (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation static method) (pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperation static method) (pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation static method) (pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation static method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ProteinCore static method) (pyrosetta.rosetta.protocols.task_operations.ProteinCoreFilterCreator method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation static method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation static method) (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB static method) (pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDBCreator method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation static method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation static method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities static method) (pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilitiesCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3Loop static method) (pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3LoopCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation static method) (pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation static method) (pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperation static method) (pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperation static method) (pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation static method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation static method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation static method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperation static method) (pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMoverCreator method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMoverCreator method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMoverCreator method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation static method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperationCreator method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMoverCreator method) (pyrosetta.rosetta.protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMoverCreator method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMoverCreator method) keys() (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.core.scoring.motif.MotifHitStats method) (pyrosetta.rosetta.protocols.indexed_structure_store._map_string_vector_Real method) (pyrosetta.rosetta.protocols.indexed_structure_store._map_string_vector_Size method) (pyrosetta.rosetta.protocols.indexed_structure_store._map_string_vector_vector_Real method) (pyrosetta.rosetta.RDKit.Dict method) (pyrosetta.rosetta.std.map_char_double method) (pyrosetta.rosetta.std.map_char_protocols_pose_sewing_movers_SeedSettings method) (pyrosetta.rosetta.std.map_char_std_pair_unsigned_long_unsigned_long_t_std_allocator_std_pair_const_char_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.map_char_std_shared_ptr_protocols_ligand_docking_LigandArea_t_std_allocator_std_pair_const_char_std_shared_ptr_protocols_ligand_docking_LigandArea_t method) (pyrosetta.rosetta.std.map_char_utility_vector1_double_std_allocator_double_t_std_allocator_std_pair_const_char_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.map_char_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_char_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.std.map_core_chemical_AA_double method) (pyrosetta.rosetta.std.map_core_chemical_AA_std_pair_double_double_t_std_allocator_std_pair_const_core_chemical_AA_std_pair_double_double_t method) (pyrosetta.rosetta.std.map_core_chemical_AA_utility_vector1_double_std_allocator_double_t_std_allocator_std_pair_const_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.map_core_environment_LocalPosition_double method) (pyrosetta.rosetta.std.map_core_id_AtomID_bool method) (pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID method) (pyrosetta.rosetta.std.map_core_id_AtomID_double method) (pyrosetta.rosetta.std.map_core_id_AtomID_unsigned_long method) (pyrosetta.rosetta.std.map_core_id_AtomID_utility_vector1_double_std_allocator_double_t_std_allocator_std_pair_const_core_id_AtomID_utility_vector1_double_std_allocator_double_t method) 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(pyrosetta.rosetta.std.map_protocols_antibody_CDRNameEnum_utility_vector1_protocols_antibody_CDRDBPose_std_allocator_protocols_antibody_CDRDBPose_t_std_allocator_std_pair_const_protocols_antibody_CDRNameEnum_utility_vector1_protocols_antibody_CDRDBPose_std_allocator_protocols_antibody_CDRDBPose_t method) (pyrosetta.rosetta.std.map_protocols_antibody_CDRNameEnum_utility_vector1_protocols_antibody_CDRDBSequence_std_allocator_protocols_antibody_CDRDBSequence_t_std_allocator_std_pair_const_protocols_antibody_CDRNameEnum_utility_vector1_protocols_antibody_CDRDBSequence_std_allocator_protocols_antibody_CDRDBSequence_t method) (pyrosetta.rosetta.std.map_protocols_antibody_clusters_CDRClusterEnum_utility_vector1_protocols_antibody_design_MutantPosition_std_allocator_protocols_antibody_design_MutantPosition_t_std_allocator_std_pair_const_protocols_antibody_clusters_CDRClusterEnum_utility_vector1_protocols_antibody_design_MutantPosition_std_allocator_protocols_antibody_design_MutantPosition_t method) (pyrosetta.rosetta.std.map_protocols_carbohydrates_GlycanSequon_std_string method) (pyrosetta.rosetta.std.map_std_pair_core_chemical_AA_core_chemical_AA_t_double_std_less_std_pair_core_chemical_AA_core_chemical_AA_t_std_allocator_std_pair_const_std_pair_core_chemical_AA_core_chemical_AA_double_t method) (pyrosetta.rosetta.std.map_std_pair_core_id_AtomID_core_id_AtomID_t_utility_vector1_double_std_allocator_double_t_std_less_std_pair_core_id_AtomID_core_id_AtomID_t_std_allocator_std_pair_const_std_pair_core_id_AtomID_core_id_AtomID_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.map_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_t_protocols_legacy_sewing_HashResult_std_less_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_t_std_allocator_std_pair_const_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_protocols_legacy_sewing_HashResult_t method) (pyrosetta.rosetta.std.map_std_pair_std_string_std_string_t_utility_vector1_core_chemical_carbohydrates_LinkageConformerData_std_allocator_core_chemical_carbohydrates_LinkageConformerData_t_std_less_std_pair_std_string_std_string_t_std_allocator_std_pair_const_std_pair_std_string_std_string_utility_vector1_core_chemical_carbohydrates_LinkageConformerData_std_allocator_core_chemical_carbohydrates_LinkageConformerData_t method) (pyrosetta.rosetta.std.map_std_pair_unsigned_long_std_string_t_utility_vector1_std_pair_numeric_xyzVector_double_double_std_allocator_std_pair_numeric_xyzVector_double_double_t_std_less_std_pair_unsigned_long_std_string_t_std_allocator_std_pair_const_std_pair_unsigned_long_std_string_utility_vector1_std_pair_numeric_xyzVector_double_double_std_allocator_std_pair_numeric_xyzVector_double_double_t method) (pyrosetta.rosetta.std.map_std_pair_unsigned_long_unsigned_long_t_std_set_protocols_sewing_hashing_LigandCoordInfo_t_std_less_std_pair_unsigned_long_unsigned_long_t_std_allocator_std_pair_const_std_pair_unsigned_long_unsigned_long_std_set_protocols_sewing_hashing_LigandCoordInfo_t method) (pyrosetta.rosetta.std.map_std_pair_unsigned_long_unsigned_long_t_unsigned_long_std_less_std_pair_unsigned_long_unsigned_long_t_std_allocator_std_pair_const_std_pair_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.map_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t_unsigned_long_std_less_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t_std_allocator_std_pair_const_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_unsigned_long_t method) (pyrosetta.rosetta.std.map_std_string_bool method) (pyrosetta.rosetta.std.map_std_string_char method) (pyrosetta.rosetta.std.map_std_string_core_chemical_AA method) (pyrosetta.rosetta.std.map_std_string_core_chemical_carbohydrates_RootData method) (pyrosetta.rosetta.std.map_std_string_core_chemical_carbohydrates_SugarModificationsNomenclatureTableRow method) (pyrosetta.rosetta.std.map_std_string_core_conformation_symmetry_VirtualCoordinate method) (pyrosetta.rosetta.std.map_std_string_core_id_NamedAtomID method) (pyrosetta.rosetta.std.map_std_string_core_io_CisPeptideInformation method) (pyrosetta.rosetta.std.map_std_string_core_io_ModifiedResidueInformation method) (pyrosetta.rosetta.std.map_std_string_core_io_nmr_ParaIon method) (pyrosetta.rosetta.std.map_std_string_core_io_nmr_SpinlabelDatabaseEntry method) (pyrosetta.rosetta.std.map_std_string_core_io_pdb_RecordType method) (pyrosetta.rosetta.std.map_std_string_core_pose_Pose method) (pyrosetta.rosetta.std.map_std_string_core_scoring_rmsd_atoms method) (pyrosetta.rosetta.std.map_std_string_double method) (pyrosetta.rosetta.std.map_std_string_float method) 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(pyrosetta.rosetta.std.map_std_string_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t_std_allocator_std_pair_const_std_string_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t method) (pyrosetta.rosetta.std.map_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t_std_allocator_std_pair_const_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t method) (pyrosetta.rosetta.std.map_std_string_std_map_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t_std_allocator_std_pair_const_std_string_std_map_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t method) (pyrosetta.rosetta.std.map_std_string_std_map_std_string_std_pair_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_pair_std_string_std_string_t_std_allocator_std_pair_const_std_string_std_map_std_string_std_pair_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_pair_std_string_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t_std_allocator_std_pair_const_std_string_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_map_unsigned_long_double_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_double_t_std_allocator_std_pair_const_std_string_std_map_unsigned_long_double_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_double_t method) (pyrosetta.rosetta.std.map_std_string_std_map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_std_string_std_map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t method) (pyrosetta.rosetta.std.map_std_string_std_map_unsigned_long_std_string_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_string_t_std_allocator_std_pair_const_std_string_std_map_unsigned_long_std_string_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_pair_core_chemical_io_merge_residue_behavior_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t_std_allocator_std_pair_const_std_string_std_pair_core_chemical_io_merge_residue_behavior_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_pair_std_string_std_string_t_std_allocator_std_pair_const_std_string_std_pair_std_string_std_string_t method) 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(pyrosetta.rosetta.std.map_std_string_std_set_std_string_t_std_allocator_std_pair_const_std_string_std_set_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_basic_MetricValueBase_t_std_allocator_std_pair_const_std_string_std_shared_ptr_basic_MetricValueBase_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_basic_resource_manager_ResourceLoaderCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_basic_resource_manager_ResourceLoaderCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_basic_resource_manager_ResourceLocatorCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_basic_resource_manager_ResourceLocatorCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_core_chemical_Metapatch_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_core_chemical_Metapatch_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_pack_daemon_VectorExpression_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_protocols_pack_daemon_VectorExpression_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_utility_tag_Tag_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_pack_palette_PackerPaletteCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pack_palette_PackerPaletteCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_pack_task_operation_ResLvlTaskOperationCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pack_task_operation_ResLvlTaskOperationCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_pack_task_operation_TaskOperationCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pack_task_operation_TaskOperationCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_pack_task_ResfileCommand_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_pose_Pose_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pose_Pose_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_scoring_motif_MotifHash_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_scoring_motif_MotifHash_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_select_jump_selector_JumpSelectorCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_select_jump_selector_JumpSelectorCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_select_residue_selector_ResidueSelector_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_select_residue_selector_ResidueSelectorCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_select_residue_selector_ResidueSelectorCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_simple_metrics_SimpleMetricCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_simple_metrics_SimpleMetricCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_numeric_expression_parser_VariableExpression_t_std_allocator_std_pair_const_std_string_std_shared_ptr_numeric_expression_parser_VariableExpression_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_FilterCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_filters_FilterCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_moves_MoverCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_moves_MoverCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_multistage_rosetta_scripts_cluster_ClusterMetricCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_multistage_rosetta_scripts_cluster_ClusterMetricCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_parser_DataLoaderCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_parser_DataLoaderCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_splice_SpliceSegment_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_splice_SpliceSegment_t method) (pyrosetta.rosetta.std.map_std_string_std_string method) (pyrosetta.rosetta.std.map_std_string_std_tuple_std_string_std_string_char_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_std_string_std_tuple_std_string_std_string_char_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_double_t method) (pyrosetta.rosetta.std.map_std_string_std_vector_std_string_t_std_allocator_std_pair_const_std_string_std_vector_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_vector_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_std_vector_double_t method) (pyrosetta.rosetta.std.map_std_string_std_vector_unsigned_long_t_std_allocator_std_pair_const_std_string_std_vector_unsigned_long_t method) (pyrosetta.rosetta.std.map_std_string_unsigned_long method) (pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_char_std_allocator_char_t_std_allocator_std_pair_const_std_string_utility_vector1_char_std_allocator_char_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_core_io_LinkInformation_std_allocator_core_io_LinkInformation_t_std_allocator_std_pair_const_std_string_utility_vector1_core_io_LinkInformation_std_allocator_core_io_LinkInformation_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_core_io_SSBondInformation_std_allocator_core_io_SSBondInformation_t_std_allocator_std_pair_const_std_string_utility_vector1_core_io_SSBondInformation_std_allocator_core_io_SSBondInformation_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_std_shared_ptr_const_core_chemical_Patch_std_allocator_std_shared_ptr_const_core_chemical_Patch_t_std_allocator_std_pair_const_std_string_utility_vector1_std_shared_ptr_const_core_chemical_Patch_std_allocator_std_shared_ptr_const_core_chemical_Patch_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_std_shared_ptr_core_conformation_Residue_std_allocator_std_shared_ptr_core_conformation_Residue_t_std_allocator_std_pair_const_std_string_utility_vector1_std_shared_ptr_core_conformation_Residue_std_allocator_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_std_string_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_unsigned_long_std_allocator_unsigned_long_t_std_allocator_std_pair_const_std_string_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.std.map_unsigned_long_bool method) (pyrosetta.rosetta.std.map_unsigned_long_char method) (pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof method) (pyrosetta.rosetta.std.map_unsigned_long_double method) (pyrosetta.rosetta.std.map_unsigned_long_numeric_xyzVector_double_t_std_allocator_std_pair_const_unsigned_long_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.map_unsigned_long_protocols_dna_DnaNeighbor method) (pyrosetta.rosetta.std.map_unsigned_long_protocols_dna_DnaPosition method) (pyrosetta.rosetta.std.map_unsigned_long_protocols_indexed_structure_store_FragmentLookupResult method) (pyrosetta.rosetta.std.map_unsigned_long_protocols_sewing_hashing_IdealContact method) (pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_pair_char_std_string_t_std_allocator_std_pair_const_unsigned_long_std_pair_char_std_string_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_pair_double_double_t_std_allocator_std_pair_const_unsigned_long_std_pair_double_double_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_set_std_string_t_std_allocator_std_pair_const_unsigned_long_std_set_std_string_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_const_core_conformation_PseudoBondCollection_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_core_conformation_PseudoBondCollection_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_const_protocols_sewing_data_storage_LigandResidue_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_protocols_sewing_data_storage_LigandResidue_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_core_conformation_carbohydrates_GlycanTree_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_core_conformation_carbohydrates_GlycanTree_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_core_fragment_FragSet_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_core_fragment_FragSet_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_core_io_PositionDdGInfo_PositionDdGInfo_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_core_io_PositionDdGInfo_PositionDdGInfo_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_core_scoring_epr_deer_metrics_DEERData_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_core_scoring_epr_deer_metrics_DEERData_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_protocols_frags_TorsionFragmentLibrary_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_frags_TorsionFragmentLibrary_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_protocols_indexed_structure_store_FragmentStore_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_indexed_structure_store_FragmentStore_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_protocols_sewing_data_storage_LigandResidue_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_sewing_data_storage_LigandResidue_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_protocols_sewing_data_storage_SmartSegment_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_sewing_data_storage_SmartSegment_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_string method) (pyrosetta.rosetta.std.map_unsigned_long_unsigned_long method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_core_id_AtomID_std_allocator_core_id_AtomID_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_core_id_AtomID_std_allocator_core_id_AtomID_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_double_std_allocator_double_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_numeric_xyzVector_double_double_std_allocator_std_pair_numeric_xyzVector_double_double_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_numeric_xyzVector_double_double_std_allocator_std_pair_numeric_xyzVector_double_double_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) KEYWDS (pyrosetta.rosetta.core.io.pdb.RecordType attribute) keyword_in_progress() (pyrosetta.rosetta.core.io.HeaderInformation method) keywords() (pyrosetta.rosetta.core.io.HeaderInformation method) kf_cexp() (in module pyrosetta.rosetta.numeric.fourier) kic_close_loops_in_samples() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close) kic_modeler_if_relevant() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) kic_sampling() (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) KicMover (class in pyrosetta.rosetta.protocols.kinematic_closure) KicMoverCreator (class in pyrosetta.rosetta.protocols.kinematic_closure) kill_antiparallel() (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) kill_parallel() (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) KinaseMover (class in pyrosetta.rosetta.protocols.enzymatic_movers) KinaseMoverCreator (class in pyrosetta.rosetta.protocols.enzymatic_movers) kind (pyrosetta.rosetta.core.scoring.packstat.Event property) KinematicAbinitio (class in pyrosetta.rosetta.protocols.abinitio) KinematicAbinitio.StageID (class in pyrosetta.rosetta.protocols.abinitio) KinematicControl (class in pyrosetta.rosetta.protocols.abinitio) KinematicMover (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) KinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) kinematics() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints 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) KinematicTaskControl (class in pyrosetta.rosetta.protocols.abinitio) KinematicWrapper (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) kinetic_energy() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) KinFunGroupTK (class in pyrosetta.rosetta.protocols.kinmatch) kink_anion_atoms() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) kink_anion_residue() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) kink_bb_Hbond() (in module pyrosetta.rosetta.protocols.antibody) kink_begin() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) kink_cation_atoms() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) kink_cation_residue() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) kink_constrain_antibody_H3() (in module pyrosetta.rosetta.protocols.antibody) kink_dihedral() (in module pyrosetta.rosetta.protocols.antibody) kink_end() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) kink_RD_Hbond() (in module pyrosetta.rosetta.protocols.antibody) kink_trp() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) kink_Trp_Hbond() (in module pyrosetta.rosetta.protocols.antibody) Kinked (pyrosetta.rosetta.protocols.antibody.H3BaseTypeEnum attribute) kinked_ (pyrosetta.rosetta.protocols.antibody_legacy.Antibody property) kinmover() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) kiss_dct() (in module pyrosetta.rosetta.numeric.fourier) kiss_dct_state (class in pyrosetta.rosetta.numeric.fourier) kiss_fft() (in module pyrosetta.rosetta.numeric.fourier) kiss_fft_cleanup() (in module pyrosetta.rosetta.numeric.fourier) kiss_fft_next_fast_size() (in module pyrosetta.rosetta.numeric.fourier) kiss_fft_split() (in module pyrosetta.rosetta.numeric.fourier) kiss_fft_state (class in pyrosetta.rosetta.numeric.fourier) kiss_fft_stride() (in module pyrosetta.rosetta.numeric.fourier) kiss_fftnd() (in module pyrosetta.rosetta.numeric.fourier) kiss_fftnd_state (class in pyrosetta.rosetta.numeric.fourier) kiss_fftndr() (in module pyrosetta.rosetta.numeric.fourier) kiss_fftndr_state (class in pyrosetta.rosetta.numeric.fourier) kiss_fftndri() (in module pyrosetta.rosetta.numeric.fourier) kiss_fftr() (in module pyrosetta.rosetta.numeric.fourier) kiss_fftr_next_fast_size_real() (in module pyrosetta.rosetta.numeric.fourier) kiss_fftr_state (class in pyrosetta.rosetta.numeric.fourier) kiss_fftri() (in module pyrosetta.rosetta.numeric.fourier) kiss_fftsplit_state (class in pyrosetta.rosetta.numeric.fourier) kiss_idct() (in module pyrosetta.rosetta.numeric.fourier) kl_divergence() (in module pyrosetta.rosetta.numeric.statistics) KMedoid (class in pyrosetta.rosetta.protocols.toolbox) KMGT() (in module pyrosetta.rosetta.protocols.sic_dock) KofNConstraint (class in pyrosetta.rosetta.core.scoring.constraints) KofNConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) Kr (pyrosetta.rosetta.core.chemical.element.Elements attribute) KromerMann (class in pyrosetta.rosetta.core.scoring.electron_density) (class in pyrosetta.rosetta.core.scoring.fiber_diffraction) KRSQuery (class in pyrosetta.rosetta.protocols.kinmatch) KRSQueryType (class in pyrosetta.rosetta.protocols.kinmatch) kT() (pyrosetta.rosetta.core.sequence.MCAligner method) Ktheta() (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParam method) kurtosis() (pyrosetta.rosetta.protocols.toolbox.InteratomicVarianceMatrix method)