Index – V

V (pyrosetta.rosetta.core.chemical.element.Elements attribute) v (pyrosetta.rosetta.core.kinematics.Stub property) (pyrosetta.rosetta.core.optimization.EItem property) v_ (pyrosetta.rosetta.core.optimization.Particle property) v_angle_width() (pyrosetta.rosetta.core.scoring.magnesium.MgKnowledgeBasedPotential method) v_indexes (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data property) val (pyrosetta.rosetta.RDKit.Dict.Pair property) val() (pyrosetta.rosetta.utility.heap method) valence_electrons_p() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) valence_electrons_s() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) valence_electrons_sp() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) valence_electrons_spd() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) valid (pyrosetta.rosetta.core.scoring.sc._RESULTS property) (pyrosetta.rosetta.utility.signals.LinkUnit property) valid() (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.JumpID method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.id.NamedStubID method) (pyrosetta.rosetta.core.id.PartialAtomID method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.utility.graph.ArrayPoolElement_double_t method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator method) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.EdgeListIterator method) (pyrosetta.rosetta.utility.graph.LowMemEdgeListConstIter method) (pyrosetta.rosetta.utility.graph.LowMemEdgeListIter method) (pyrosetta.rosetta.utility.signals.Link method) (pyrosetta.rosetta.utility.tag.XMLValidationOutput method) valid_anchors() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) valid_basestep_start() (pyrosetta.rosetta.protocols.dna.DNAParameters method) valid_chain_info() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) valid_ends() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) valid_names_string() (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) valid_next_grid_point() (pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch method) valid_peptide_chain() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) valid_receptor_chain() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) valid_ref_start_struct() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) valid_res_pair() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) valid_ss() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) validate() (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_bool_t static method) (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_double_t static method) (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_float_t static method) (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_int_t static method) (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_long_t static method) (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_unsigned_int_t static method) (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_unsigned_long_t static method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChainNumbering method) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds method) validate_beta() (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory static method) validate_dunbrack_binary() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) validate_input() (pyrosetta.rosetta.core.sequence.Aligner method) (pyrosetta.rosetta.core.sequence.MCAligner method) (pyrosetta.rosetta.core.sequence.NWAligner method) (pyrosetta.rosetta.core.sequence.SWAligner method) validate_input_script_against_xsd() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) validate_loop_start_stop() (in module pyrosetta.rosetta.protocols.loops) validate_ramachandran_hash() (pyrosetta.rosetta.protocols.features.BetaTurnDetection method) validate_residue_selectors() (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover static method) validate_residue_type() (pyrosetta.rosetta.core.chemical.MutableResidueType method) validate_talaris() (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory static method) validate_template() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) validate_xml_against_schema() (pyrosetta.rosetta.utility.tag.XMLValidator method) validate_xml_against_xsd() (in module pyrosetta.rosetta.utility.tag) validator() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsSchemaValidator method) vall_key() (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) vall_library_from_file() (in module pyrosetta.rosetta.core.fragment.picking_old.vall) vall_memory_usage() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) vall_torsions_file() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) VallChunk (class in pyrosetta.rosetta.protocols.frag_picker) VallChunkFilter (class in pyrosetta.rosetta.protocols.frag_picker) vallChunksFromLibraries() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) vallChunksFromLibrary() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) VallData (class in pyrosetta.rosetta.protocols.frags) VallFragmentEval (class in pyrosetta.rosetta.core.fragment.picking_old.vall.eval) VallFragmentGen (class in pyrosetta.rosetta.core.fragment.picking_old.vall.gen) VallFragmentScore (class in pyrosetta.rosetta.core.fragment.picking_old.vall.scores) VallLibrarian (class in pyrosetta.rosetta.core.fragment.picking_old.vall) VallLibrary (class in pyrosetta.rosetta.core.fragment.picking_old.vall) vallNumLines() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) VallProvider (class in pyrosetta.rosetta.protocols.frag_picker) VallResidue (class in pyrosetta.rosetta.core.fragment.picking_old.vall) (class in pyrosetta.rosetta.protocols.frag_picker) VallResidues (class in pyrosetta.rosetta.core.fragment.picking_old.vall) VallSection (class in pyrosetta.rosetta.core.fragment.picking_old.vall) VallSections (class in pyrosetta.rosetta.core.fragment.picking_old.vall) Value (class in pyrosetta.rosetta.utility.py) value (pyrosetta.rosetta.basic.citation_manager.CitationFormat property) (pyrosetta.rosetta.basic.citation_manager.CitedModuleType property) (pyrosetta.rosetta.basic.mpi.listener_tags property) (pyrosetta.rosetta.basic.mpi.mpi_tags property) (pyrosetta.rosetta.basic.ProfTag property) (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_bool_t property) (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_double_t property) (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_float_t property) (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_int_t property) (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_long_t property) (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_unsigned_int_t property) (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_unsigned_long_t property) (pyrosetta.rosetta.basic.thread_manager.RosettaThreadRequestOriginatingLevel property) (pyrosetta.rosetta.basic.TracerPriority property) (pyrosetta.rosetta.core.chemical.AA property) (pyrosetta.rosetta.core.chemical.Ancestor property) (pyrosetta.rosetta.core.chemical.AtomProperty property) (pyrosetta.rosetta.core.chemical.BondAromaticity property) (pyrosetta.rosetta.core.chemical.BondConjugability property) (pyrosetta.rosetta.core.chemical.BondIsometry property) (pyrosetta.rosetta.core.chemical.BondName property) (pyrosetta.rosetta.core.chemical.BondOrder property) (pyrosetta.rosetta.core.chemical.BondRingness property) (pyrosetta.rosetta.core.chemical.ElectronConfiguration.AngularMomentumQuantumNumber property) (pyrosetta.rosetta.core.chemical.ElectronConfiguration.PrincipalQuantumNumber property) (pyrosetta.rosetta.core.chemical.element.Elements property) (pyrosetta.rosetta.core.chemical.Element.Properties property) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.AtomicOrbitalTypes property) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.HybridOrbitalType property) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType property) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties property) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference property) (pyrosetta.rosetta.core.chemical.GreekDistance property) (pyrosetta.rosetta.core.chemical.Hybridization property) (pyrosetta.rosetta.core.chemical.ICoordAtomIDType property) (pyrosetta.rosetta.core.chemical.io.merge_residue_behavior property) (pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus property) (pyrosetta.rosetta.core.chemical.orbitals.orbital_type_enum property) (pyrosetta.rosetta.core.chemical.ResidueProperty property) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation property) (pyrosetta.rosetta.core.chemical.rings.CPParameter property) (pyrosetta.rosetta.core.chemical.rings.RingSaturationType property) (pyrosetta.rosetta.core.chemical.rna.BaseDoubletOrientation property) (pyrosetta.rosetta.core.chemical.rna.BaseEdge property) (pyrosetta.rosetta.core.chemical.rna.BaseStackWhichSide property) (pyrosetta.rosetta.core.chemical.rna.ChiState property) (pyrosetta.rosetta.core.chemical.rna.LW_BaseDoubletOrientation property) (pyrosetta.rosetta.core.chemical.rna.PuckerState property) (pyrosetta.rosetta.core.chemical.rna.RNA_Torsion property) (pyrosetta.rosetta.core.chemical.TypeSetMode property) (pyrosetta.rosetta.core.chemical.VariantType property) (pyrosetta.rosetta.core.conformation.membrane.MEM property) (pyrosetta.rosetta.core.conformation.membrane.MP_GEOMETRY_TRANSITION property) (pyrosetta.rosetta.core.conformation.membrane.Orientation property) (pyrosetta.rosetta.core.conformation.parametric.ParameterType property) (pyrosetta.rosetta.core.conformation.parametric.RealPerturbationType property) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin property) (pyrosetta.rosetta.core.conformation.residue_datacache.ResidueDataCacheIndex property) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum property) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag property) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag property) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag property) (pyrosetta.rosetta.core.conformation.Strategy property) (pyrosetta.rosetta.core.conformation.symmetry.dof_type property) (pyrosetta.rosetta.core.conformation.symmetry.SlideCriteriaType property) (pyrosetta.rosetta.core.conformation.symmetry.SlideType property) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType property) (pyrosetta.rosetta.core.fragment.rna._RNA_MatchType_ property) (pyrosetta.rosetta.core.fragment.rna.SYN_ANTI_RESTRICTION property) (pyrosetta.rosetta.core.id.DOF_Type property) (pyrosetta.rosetta.core.id.MainchainTorsionType property) (pyrosetta.rosetta.core.id.TorsionType property) (pyrosetta.rosetta.core.import_pose.FileType property) (pyrosetta.rosetta.core.io.HeaderInformation.CompoundToken property) (pyrosetta.rosetta.core.io.mmtf.ExtraDataEnum property) (pyrosetta.rosetta.core.io.pdb.Field property) (pyrosetta.rosetta.core.io.pdb.RecordType property) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile.NumberingSystem property) (pyrosetta.rosetta.core.io.rcsb.ExperimentalTechnique property) (pyrosetta.rosetta.core.io.RemarkInfo property) (pyrosetta.rosetta.core.io.silent.SharedSilentDataType property) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine property) (pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobianTypeEnum property) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergyRamping property) (pyrosetta.rosetta.core.pack.interaction_graph.ResiduePairEvalType property) (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour property) (pyrosetta.rosetta.core.pack.rotamer_set.BumpSelectorDecision property) (pyrosetta.rosetta.core.pack.task.ExtraRotSample property) (pyrosetta.rosetta.core.pack.task.PackerTaskSymmetryStatus property) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum property) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType property) (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType property) (pyrosetta.rosetta.core.pose.PoseCoordPickMode property) (pyrosetta.rosetta.core.pose.rna.RNA_ReactivityType property) (pyrosetta.rosetta.core.pose.rna.StubStubType property) (pyrosetta.rosetta.core.pose.rna.Terminus property) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction property) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES property) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE property) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType property) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType property) (pyrosetta.rosetta.core.scoring.ContextGraphType property) (pyrosetta.rosetta.core.scoring.DC.DC_TYPE property) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideDerivativeAtom property) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum property) (pyrosetta.rosetta.core.scoring.etable.count_pair.CPCrossoverBehavior property) (pyrosetta.rosetta.core.scoring.etable.count_pair.CPResidueConnectionType property) (pyrosetta.rosetta.core.scoring.geometric_solvation.OccFitParam property) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType property) (pyrosetta.rosetta.core.scoring.hbonds.HBDerivType property) (pyrosetta.rosetta.core.scoring.hbonds.HBDonChemType property) (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType property) (pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType property) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType property) (pyrosetta.rosetta.core.scoring.hbonds.HBSeqSep property) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond property) (pyrosetta.rosetta.core.scoring.methods.EnergyMethods property) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodType property) (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType property) (pyrosetta.rosetta.core.scoring.min_pair_data property) (pyrosetta.rosetta.core.scoring.min_single_data property) (pyrosetta.rosetta.core.scoring.motif.MotifMatchOverlapReq property) (pyrosetta.rosetta.core.scoring.motif.RM_Type property) (pyrosetta.rosetta.core.scoring.motif.RPM_Type property) (pyrosetta.rosetta.core.scoring.MultipoleAxisType property) (pyrosetta.rosetta.core.scoring.netcharge_energy.TailFunction property) (pyrosetta.rosetta.core.scoring.nmr.EULER_CONVENTION property) (pyrosetta.rosetta.core.scoring.nmr.NMR_VALUE_AVERAGING_TYPE property) (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel.CONFORMER_FILTER property) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet.COMPUTATION_TYPE property) (pyrosetta.rosetta.core.scoring.nmr.PRE_RATE_TYPE property) (pyrosetta.rosetta.core.scoring.nmr.PRE_SPIN_TYPE property) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet.COMPUTATION_TYPE property) (pyrosetta.rosetta.core.scoring.nmr.RDC_NORM_TYPE property) (pyrosetta.rosetta.core.scoring.nmr.RDC_TYPE property) (pyrosetta.rosetta.core.scoring.nmr.SINGLE_NMR_VALUE_WEIGHTING property) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsLookup.h_type property) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics.orbital_type_name property) (pyrosetta.rosetta.core.scoring.packstat.EventType property) (pyrosetta.rosetta.core.scoring.ProteinTorsion property) (pyrosetta.rosetta.core.scoring.Rama_Table_Type property) (pyrosetta.rosetta.core.scoring.RDC.RDC_TYPE property) (pyrosetta.rosetta.core.scoring.rmsd_atoms property) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem property) (pyrosetta.rosetta.core.scoring.rna.RNA_MotifType property) (pyrosetta.rosetta.core.scoring.sasa.SasaMethodEnum property) (pyrosetta.rosetta.core.scoring.sasa.SasaMethodHPMode property) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii property) (pyrosetta.rosetta.core.scoring.ScoreType property) (pyrosetta.rosetta.core.select.movemap.move_map_action property) (pyrosetta.rosetta.core.select.residue_selector.basic_selection_logic property) (pyrosetta.rosetta.core.select.residue_selector.slice_enums.OutOfBoundsMode property) (pyrosetta.rosetta.core.select.residue_selector.slice_enums.SliceMode property) (pyrosetta.rosetta.core.sequence.AlignMove property) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricMode property) (pyrosetta.rosetta.core.simple_metrics.metrics.summary_type property) (pyrosetta.rosetta.cppdb.backend.result.next_row property) (pyrosetta.rosetta.numeric.conversions.AngleUnit property) (pyrosetta.rosetta.numeric.expression_parser.TokenType property) (pyrosetta.rosetta.numeric.interpolation.CatmullRomSplineBoundaryType property) (pyrosetta.rosetta.numeric.interpolation.spline.BorderFlag property) (pyrosetta.rosetta.numeric.RocStatus property) (pyrosetta.rosetta.protocols.abinitio.abscript.StageID property) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio.StageID property) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints.StageID property) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax.IterationStage property) (pyrosetta.rosetta.protocols.abinitio.IterativeBase.IterationStage property) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid.IterationStage property) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom.IterationStage property) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper.StageID property) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio.StageID property) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio.StageID property) (pyrosetta.rosetta.protocols.abinitio.StageID property) (pyrosetta.rosetta.protocols.analysis.InterfaceRegion property) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingSchemeEnum property) (pyrosetta.rosetta.protocols.antibody.AntibodyRegionEnum property) (pyrosetta.rosetta.protocols.antibody.CDRDefinitionEnum property) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum property) (pyrosetta.rosetta.protocols.antibody.CDRNameEnum property) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum property) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocolEnum property) (pyrosetta.rosetta.protocols.antibody.design.MinTypeEnum property) (pyrosetta.rosetta.protocols.antibody.design.SeqDesignStrategyEnum property) (pyrosetta.rosetta.protocols.antibody.H3BaseTypeEnum property) (pyrosetta.rosetta.protocols.antibody.LightChainTypeEnum property) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum property) (pyrosetta.rosetta.protocols.buns.CALCULATORMODE property) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operation property) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2.ScoreType property) (pyrosetta.rosetta.protocols.canonical_sampling.InterpolationType property) (pyrosetta.rosetta.protocols.canonical_sampling.TorsionSpecStyle property) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSequon property) (pyrosetta.rosetta.protocols.carbohydrates.QuenchDirection property) (pyrosetta.rosetta.protocols.cluster.calibur.ADJ_LIST_MODE property) (pyrosetta.rosetta.protocols.cluster.calibur.EST_THRESHOLD_MODE property) (pyrosetta.rosetta.protocols.cluster.calibur.INPUT_FILE_TYPE property) (pyrosetta.rosetta.protocols.comparative_modeling.features.SSType property) (pyrosetta.rosetta.protocols.comparative_modeling.features.TorsionBin property) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover.AtomSelector property) (pyrosetta.rosetta.protocols.cryst.SpacegroupSetting property) (pyrosetta.rosetta.protocols.cryst.WallpaperGroupSetting property) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker property) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase_Metal property) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase_MetalLigand property) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMoverMode property) (pyrosetta.rosetta.protocols.cyclic_peptide.PSM_StubMode property) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HIERARCHICAL_HYBRID_JD_MPI_SORT_TYPE property) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type property) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing.PairingType property) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing.PairingType property) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentCounts.SegmentType property) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing.PairingType property) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation property) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing.PairingType property) (pyrosetta.rosetta.protocols.docking.DHR_Type property) (pyrosetta.rosetta.protocols.energy_based_clustering.EBC_ClusterType 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(pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray5D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_float_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_float_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_float_ObjexxFCL_FArray5D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray4D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray5D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_numeric_xyzVector_double_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_ObjexxFCL_FArray1D_int_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_ObjexxFCL_FArray2D_float__star__ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_ObjexxFCL_ubyte_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_std_complex_double_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_std_string_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_std_string_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_std_vector_unsigned_long_std_allocator_unsigned_long_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_char_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_char_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_char_ObjexxFCL_FArray4D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_long_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_long_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_long_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_double_std_allocator_double_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_double_std_allocator_double_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_unsigned_int_std_allocator_unsigned_int_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.utility.Bound_bool_t method) (pyrosetta.rosetta.utility.Bound_double_t method) (pyrosetta.rosetta.utility.Bound_int_t method) (pyrosetta.rosetta.utility.Bound_std_string_t method) (pyrosetta.rosetta.utility.Bound_utility_file_FileName_t method) (pyrosetta.rosetta.utility.Bound_utility_file_PathName_t method) (pyrosetta.rosetta.utility.libsvm.Svm_node_rosetta method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.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.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) value_ (pyrosetta.rosetta.core.simple_metrics.TestRealMetric property) (pyrosetta.rosetta.utility.json_spirit.Pair_impl_utility_json_spirit_Config_vector_std_string_t property) (pyrosetta.rosetta.utility.py.OverloadTest property) value_attribute_type_for_option() (in module pyrosetta.rosetta.protocols.jd3) value_comp() (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairSet 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) value_deriv() (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) Value_impl_utility_json_spirit_Config_map_std_basic_string_wchar_t_t (class in pyrosetta.rosetta.utility.json_spirit) Value_impl_utility_json_spirit_Config_map_std_string_t (class in pyrosetta.rosetta.utility.json_spirit) Value_impl_utility_json_spirit_Config_vector_std_basic_string_wchar_t_t (class in pyrosetta.rosetta.utility.json_spirit) Value_impl_utility_json_spirit_Config_vector_std_string_t (class in pyrosetta.rosetta.utility.json_spirit) value_max() (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) value_min() (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) value_or() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.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.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) value_passes() (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator method) value_range() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) value_samples() (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) value_set() (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) value_string() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.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.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) Value_type (class in pyrosetta.rosetta.utility.json_spirit) value_was_set() (pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.Parameter method) (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) ValueEvaluator (class in pyrosetta.rosetta.protocols.enzdes) ValueEvaluator.CompareMode (class in pyrosetta.rosetta.protocols.enzdes) values() (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.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) (pyrosetta.rosetta.std.map_core_scoring_rmsd_atoms_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_core_scoring_rmsd_atoms_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.std.map_core_scoring_ScoreType_double method) (pyrosetta.rosetta.std.map_int_int method) (pyrosetta.rosetta.std.map_int_protocols_legacy_sewing_Model method) (pyrosetta.rosetta.std.map_int_utility_vector0_float_std_allocator_float_t_std_allocator_std_pair_const_int_utility_vector0_float_std_allocator_float_t method) (pyrosetta.rosetta.std.map_protocols_antibody_CDRNameEnum_protocols_loops_Loop method) (pyrosetta.rosetta.std.map_protocols_antibody_CDRNameEnum_utility_vector1_core_chemical_AA_std_allocator_core_chemical_AA_t_std_allocator_std_pair_const_protocols_antibody_CDRNameEnum_utility_vector1_core_chemical_AA_std_allocator_core_chemical_AA_t method) (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) (pyrosetta.rosetta.std.map_std_string_int method) (pyrosetta.rosetta.std.map_std_string_numeric_interpolation_spline_LinearFunction method) (pyrosetta.rosetta.std.map_std_string_numeric_xyzVector_double_t_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.map_std_string_protocols_denovo_design_components_Alias method) (pyrosetta.rosetta.std.map_std_string_protocols_scoring_methods_pcs2_PcsInputFile method) (pyrosetta.rosetta.std.map_std_string_protocols_scoring_methods_pcs_PCS_file_data method) (pyrosetta.rosetta.std.map_std_string_protocols_scoring_methods_pcsTs1_PCS_file_data_Ts1 method) (pyrosetta.rosetta.std.map_std_string_protocols_scoring_methods_pcsTs2_PCS_file_data_Ts2 method) (pyrosetta.rosetta.std.map_std_string_protocols_scoring_methods_pcsTs3_PCS_file_data_Ts3 method) (pyrosetta.rosetta.std.map_std_string_protocols_scoring_methods_pcsTs4_PCS_file_data_Ts4 method) (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) 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(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) 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(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) (pyrosetta.rosetta.std.map_std_string_std_pair_utility_vector1_std_pair_std_string_std_string_std_allocator_std_pair_std_string_std_string_utility_vector1_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_std_allocator_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_utility_vector1_std_pair_std_string_std_string_std_allocator_std_pair_std_string_std_string_utility_vector1_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_std_allocator_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_set_std_shared_ptr_basic_datacache_WriteableCacheableData_t_std_allocator_std_pair_const_std_string_std_set_std_shared_ptr_basic_datacache_WriteableCacheableData_t method) (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) values_for_aa() (pyrosetta.rosetta.core.sequence.MatrixScoringScheme method) VanillaJobDistributor (class in pyrosetta.rosetta.protocols.jd3.job_distributors) VARIABLE (pyrosetta.rosetta.numeric.expression_parser.TokenType attribute) variable_expression() (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction method) (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunctionDriver method) (pyrosetta.rosetta.protocols.pack_daemon.EntityFunc method) variable_name() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) VariableExpression (class in pyrosetta.rosetta.numeric.expression_parser) variables() (pyrosetta.rosetta.numeric.expression_parser.BooleanExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.SimpleExpressionCreator method) VariableSubstitutionPair (class in pyrosetta.rosetta.protocols.relax) VariableToken (class in pyrosetta.rosetta.numeric.expression_parser) VariableVectorExpression (class in pyrosetta.rosetta.protocols.pack_daemon) VarianceStatisticsArchive (class in pyrosetta.rosetta.protocols.jd2.archive) variant_exceptions() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) variant_type_enums() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) variant_types() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.pose.MiniPose method) variant_types_list() (pyrosetta.rosetta.core.pose.MiniPose method) VariantKey_utility_options_OptionKey_t (class in pyrosetta.rosetta.utility.keys) VariantOption_utility_options_ScalarOption_t (class in pyrosetta.rosetta.utility.options) VariantOption_utility_options_VectorOption_t (class in pyrosetta.rosetta.utility.options) variants() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) variants_in_sets() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) variants_match() (in module pyrosetta.rosetta.core.chemical) variants_match_with_exceptions() (in module pyrosetta.rosetta.core.chemical) VariantType (class in pyrosetta.rosetta.core.chemical) VarLengthBuild (class in pyrosetta.rosetta.protocols.forge.components) VARS (pyrosetta.rosetta.protocols.sparta.GDB property) VARS_str (pyrosetta.rosetta.protocols.sparta.GDB property) VARS_str_parser() (pyrosetta.rosetta.protocols.sparta.GDB method) vars_to_dofs() (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) VarsNumber (pyrosetta.rosetta.protocols.sparta.GDB property) VarSolDistSasaCalculator (class in pyrosetta.rosetta.protocols.vardist_solaccess) VarSolDRotamerDots (class in pyrosetta.rosetta.protocols.vardist_solaccess) vary_bond_geometry() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) vary_loop_length_frequency() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) vary_polar_hydrogen_geometry() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) vary_rna_bond_geometry() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) vary_stepsize() (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) VaryLoopLengthMover (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) vbpos() (pyrosetta.rosetta.protocols.motifs.MotifHit method) vd_to_index() (pyrosetta.rosetta.core.chemical.rdkit.RestypeToRDMol method) VDDistanceMatrix (class in pyrosetta.rosetta.core.chemical) vdw (pyrosetta.rosetta.core.scoring.ScoreType attribute) VDW_align_res (pyrosetta.rosetta.core.pose.rna.VDW_RepScreenInfo property) vdw_atom_list() (pyrosetta.rosetta.core.scoring.rna.RNA_AtomVDW method) VDW_ATR_REP (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) VDW_BIN (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) VDW_BinScreener (class in pyrosetta.rosetta.protocols.stepwise.screener) vdw_cached_rep_screen_info_is_setup() (in module pyrosetta.rosetta.protocols.scoring) VDW_CachedRepScreenInfo (class in pyrosetta.rosetta.protocols.scoring) vdw_calculation_annotated_sequence() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) VDW_Energy (class in pyrosetta.rosetta.core.scoring.vdwaals) VDW_ENERGY (pyrosetta.rosetta.basic.ProfTag attribute) VDW_EnergyCreator (class in pyrosetta.rosetta.core.scoring.vdwaals) VDW_Grid (class in pyrosetta.rosetta.core.pose.rna) VDW_GridEnergy (class in pyrosetta.rosetta.protocols.scoring) VDW_GridEnergyCreator (class in pyrosetta.rosetta.protocols.scoring) VDW_ignore_res (pyrosetta.rosetta.core.pose.rna.VDW_RepScreenInfo property) vdw_method (pyrosetta.rosetta.core.scoring.methods.EnergyMethods attribute) VDW_pose (pyrosetta.rosetta.core.pose.rna.VDW_RepScreenInfo property) VDW_RAD (pyrosetta.rosetta.protocols.sparta.PDB property) VDW_rep_alignment_RMSD_CUTOFF() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) VDW_rep_delete_matching_res() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) VDW_rep_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker method) vdw_rep_screen_include_sidechains() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) VDW_REP_SCREEN_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) VDW_rep_screen_info() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) VDW_rep_screen_info_list() (pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo method) VDW_rep_screen_physical_pose_clash_dist_cutoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) VDW_rep_screen_with_act_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker method) VDW_RepScreenInfo (class in pyrosetta.rosetta.core.pose.rna) vdw_res_data (pyrosetta.rosetta.core.scoring.min_single_data attribute) vdw_respair_data (pyrosetta.rosetta.core.scoring.min_pair_data attribute) VDW_screen_bin() (pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo method) vdw_tinker_lr (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) vdw_type() (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) vdw_weight() (pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieEvaluator method) VDWaalsRadius (pyrosetta.rosetta.core.chemical.Element attribute) (pyrosetta.rosetta.core.chemical.Element.Properties attribute) VdWaalsRadiusCSD (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) VDWAtom (class in pyrosetta.rosetta.core.scoring.vdwaals) VdwGrid (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) VdwGridCreator (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) VDWTINKER_POSE_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) VDWTINKER_ROTAMER_SET_INFO (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum attribute) VdWTinkerEnergy (class in pyrosetta.rosetta.core.energy_methods) VdWTinkerEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) VdWTinkerPoseInfo (class in pyrosetta.rosetta.core.scoring) VdWTinkerPotential (class in pyrosetta.rosetta.core.scoring) VdWTinkerResidueInfo (class in pyrosetta.rosetta.core.scoring) VdWTinkerRotamerSetInfo (class in pyrosetta.rosetta.core.scoring) VDWTrieCountPair1B (class in pyrosetta.rosetta.core.scoring.vdwaals) VDWTrieEvaluator (class in pyrosetta.rosetta.core.scoring.vdwaals) Vec1Hash (class in pyrosetta.rosetta.protocols.genetic_algorithm) Vec3 (class in pyrosetta.rosetta.protocols.sic_dock) vec3_to_stub() (in module pyrosetta.rosetta.protocols.sic_dock) vec_distance() (in module pyrosetta.rosetta.numeric.kdtree) vecAB() (pyrosetta.rosetta.protocols.surface_docking.SurfaceParameters method) vecAC() (pyrosetta.rosetta.protocols.surface_docking.SurfaceParameters method) vector() (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) vector0_core_conformation_ppo_torsion_bin (class in pyrosetta.rosetta.utility) vector0_core_id_AtomID_Map_bool_t (class in pyrosetta.rosetta.utility) vector0_core_io_AtomInformation (class in pyrosetta.rosetta.utility) vector0_double (class in pyrosetta.rosetta.utility) vector0_float (class in pyrosetta.rosetta.utility) vector0_int (class in pyrosetta.rosetta.utility) vector0_numeric_xyzVector_double_t (class in pyrosetta.rosetta.utility) vector0_protocols_flexpack_interaction_graph_FlexbbSparseMatrixIndex (class in pyrosetta.rosetta.utility) vector0_std_list_std_shared_ptr_utility_SimulateMPIMessage_t (class in pyrosetta.rosetta.utility) vector0_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t (class in pyrosetta.rosetta.utility) vector0_std_pair_float_float_t (class in pyrosetta.rosetta.utility) vector0_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t (class in pyrosetta.rosetta.utility) vector0_std_shared_ptr_const_utility_tag_Tag_t (class in pyrosetta.rosetta.utility) vector0_std_shared_ptr_core_kinematics_tree_Atom_t (class in pyrosetta.rosetta.utility) vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t (class in pyrosetta.rosetta.utility) vector0_std_shared_ptr_protocols_moves_Mover_t (class in pyrosetta.rosetta.utility) vector0_std_string (class in pyrosetta.rosetta.utility) vector0_unsigned_char (class in pyrosetta.rosetta.utility) vector0_unsigned_long (class in pyrosetta.rosetta.utility) vector0_utility_fixedsizearray0_double_3_t (class in pyrosetta.rosetta.utility) vector0_utility_fixedsizearray0_double_5_t (class in pyrosetta.rosetta.utility) vector0_utility_fixedsizearray0_utility_fixedsizearray0_double_3_3_t (class in pyrosetta.rosetta.utility) vector0_utility_fixedsizearray0_utility_fixedsizearray0_double_5_5_t (class in pyrosetta.rosetta.utility) vector0_utility_fixedsizearray1_double_16_t (class in pyrosetta.rosetta.utility) vector0_utility_vector0_core_io_AtomInformation_std_allocator_core_io_AtomInformation_t (class in pyrosetta.rosetta.utility) vector0_utility_vector0_double_std_allocator_double_t (class in pyrosetta.rosetta.utility) vector0_utility_vector0_int_std_allocator_int_t (class in pyrosetta.rosetta.utility) vector0_utility_vector0_std_list_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_list_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_shared_ptr_utility_SimulateMPIMessage_t (class in pyrosetta.rosetta.utility) vector0_utility_vector0_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_std_allocator_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t (class in pyrosetta.rosetta.utility) vector0_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.utility) vector0_utility_vector1_std_pair_int_int_std_allocator_std_pair_int_int_t (class in pyrosetta.rosetta.utility) vector0_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.utility) Vector1() (in module pyrosetta) vector1_basic_citation_manager_AuthorNames (class in pyrosetta.rosetta.utility) vector1_basic_database_schema_generator_Column (class in pyrosetta.rosetta.utility) vector1_basic_database_schema_generator_ForeignKey (class in pyrosetta.rosetta.utility) vector1_basic_database_schema_generator_Index (class in pyrosetta.rosetta.utility) vector1_basic_sampling_orientations_QuatDBMetadata (class in pyrosetta.rosetta.utility) vector1_bool (class in pyrosetta.rosetta.utility) vector1_char (class in pyrosetta.rosetta.utility) vector1_const_utility_vector1_int_std_allocator_int__star_t (class in pyrosetta.rosetta.utility) vector1_core_chemical_AA (class in pyrosetta.rosetta.utility) vector1_core_chemical_Adduct (class in pyrosetta.rosetta.utility) vector1_core_chemical_AtomICoor (class in pyrosetta.rosetta.utility) vector1_core_chemical_AtomType (class in pyrosetta.rosetta.utility) vector1_core_chemical_BondName (class in pyrosetta.rosetta.utility) vector1_core_chemical_io_merge_residue_behavior (class in pyrosetta.rosetta.utility) vector1_core_chemical_MutableResidueConnection (class in pyrosetta.rosetta.utility) vector1_core_chemical_ResConnID (class in pyrosetta.rosetta.utility) vector1_core_chemical_ResidueConnection (class in pyrosetta.rosetta.utility) vector1_core_chemical_ResidueProperty (class in pyrosetta.rosetta.utility) vector1_core_chemical_rings_RingConformer (class in pyrosetta.rosetta.utility) vector1_core_chemical_rings_RingSaturationType (class in pyrosetta.rosetta.utility) vector1_core_chemical_rna_GaussianParameter (class in pyrosetta.rosetta.utility) vector1_core_chemical_rna_PuckerState (class in pyrosetta.rosetta.utility) vector1_core_chemical_VariantType (class in pyrosetta.rosetta.utility) vector1_core_conformation_Atom (class in pyrosetta.rosetta.utility) vector1_core_conformation_PseudoBond (class in pyrosetta.rosetta.utility) vector1_core_conformation_signals_LengthEvent (class in pyrosetta.rosetta.utility) vector1_core_conformation_UltraLightResidue (class in pyrosetta.rosetta.utility) vector1_core_fragment_FragData (class in pyrosetta.rosetta.utility) vector1_core_fragment_picking_old_vall_scores_VallFragmentScore (class in pyrosetta.rosetta.utility) vector1_core_fragment_picking_old_vall_VallResidue (class in pyrosetta.rosetta.utility) vector1_core_fragment_picking_old_vall_VallSection (class in pyrosetta.rosetta.utility) vector1_core_fragment_rna_SYN_ANTI_RESTRICTION (class in pyrosetta.rosetta.utility) vector1_core_id_AtomID (class in pyrosetta.rosetta.utility) vector1_core_id_AtomID_Map_bool_t (class in pyrosetta.rosetta.utility) vector1_core_id_AtomID_Map_core_id_TorsionID_t (class in pyrosetta.rosetta.utility) vector1_core_id_AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t (class in pyrosetta.rosetta.utility) vector1_core_id_DOF_ID (class in pyrosetta.rosetta.utility) vector1_core_id_NamedAtomID (class in pyrosetta.rosetta.utility) vector1_core_id_TorsionID (class in pyrosetta.rosetta.utility) vector1_core_id_TorsionID_Range (class in pyrosetta.rosetta.utility) vector1_core_io_AtomInformation (class in pyrosetta.rosetta.utility) vector1_core_io_HELIXInformation (class in pyrosetta.rosetta.utility) vector1_core_io_LinkInformation (class in pyrosetta.rosetta.utility) vector1_core_io_ResidueInformation (class in pyrosetta.rosetta.utility) vector1_core_io_SHEETInformation (class in pyrosetta.rosetta.utility) vector1_core_io_silent_SilentEnergy (class in pyrosetta.rosetta.utility) vector1_core_io_SSBondInformation (class in pyrosetta.rosetta.utility) vector1_core_kinematics_AtomWithDOFChange (class in pyrosetta.rosetta.utility) vector1_core_kinematics_Edge (class in pyrosetta.rosetta.utility) vector1_core_kinematics_Jump (class in pyrosetta.rosetta.utility) vector1_core_kinematics_RT (class in pyrosetta.rosetta.utility) vector1_core_kinematics_Stub (class in pyrosetta.rosetta.utility) vector1_core_optimization_DerivCheckDataPoint (class in pyrosetta.rosetta.utility) vector1_core_optimization_DOF_DataPoint (class in pyrosetta.rosetta.utility) vector1_core_pack_annealer_PointDwell (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_1_1_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_1_2_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_1_3_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_1_4_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_1_5_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_2_1_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_2_2_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_2_3_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_2_4_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_2_5_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_3_1_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_3_2_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_3_3_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_3_4_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_3_5_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_4_1_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_4_2_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_4_3_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_4_4_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_4_5_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_5_1_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_5_2_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_5_3_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_5_4_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamer_5_5_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_DunbrackRotamerSampleData (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_double_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_double_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_double_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_double_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_double_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_double_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_double_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_double_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_double_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_double_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t (class in pyrosetta.rosetta.utility) vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbond (class in pyrosetta.rosetta.utility) vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup (class in pyrosetta.rosetta.utility) vector1_core_pack_guidance_scoreterms_sap_BlockParam (class in pyrosetta.rosetta.utility) vector1_core_pack_interaction_graph_DotSphere (class in pyrosetta.rosetta.utility) vector1_core_pack_interaction_graph_exposed_hydrophobic_data (class in pyrosetta.rosetta.utility) vector1_core_pack_interaction_graph_RotamerDots (class in pyrosetta.rosetta.utility) vector1_core_pack_interaction_graph_SparseMatrixIndex (class in pyrosetta.rosetta.utility) vector1_core_pack_rotamer_set_ContinuousRotamerSet (class in pyrosetta.rosetta.utility) vector1_core_pack_scmin_ResidueAtomTreeCollectionMomento (class in pyrosetta.rosetta.utility) vector1_core_pack_task_operation_ResiduePDBIndexIs_ChainPos (class in pyrosetta.rosetta.utility) vector1_core_pack_task_ResidueLevelTask_ (class in pyrosetta.rosetta.utility) vector1_core_pose_PDBInfo_AtomRecord (class in pyrosetta.rosetta.utility) vector1_core_pose_PDBInfo_ResidueRecord (class in pyrosetta.rosetta.utility) vector1_core_pose_Pose (class in pyrosetta.rosetta.utility) vector1_core_pose_rna_Atom_Bin (class in pyrosetta.rosetta.utility) vector1_core_pose_rna_BasePair (class in pyrosetta.rosetta.utility) vector1_core_pose_rna_BaseStack (class in pyrosetta.rosetta.utility) vector1_core_pose_rna_RNA_Datum (class in pyrosetta.rosetta.utility) vector1_core_pose_rna_RNA_Reactivity (class in pyrosetta.rosetta.utility) vector1_core_pose_rna_RNA_SuiteInfo (class in pyrosetta.rosetta.utility) vector1_core_pose_rna_VDW_RepScreenInfo (class in pyrosetta.rosetta.utility) vector1_core_pose_UnrecognizedAtomRecord (class in pyrosetta.rosetta.utility) vector1_core_scoring_bin_transitions_BT_PROPERTIES (class in pyrosetta.rosetta.utility) vector1_core_scoring_CSA (class in pyrosetta.rosetta.utility) vector1_core_scoring_DC (class in pyrosetta.rosetta.utility) vector1_core_scoring_DerivVectorPair (class in pyrosetta.rosetta.utility) vector1_core_scoring_disulfides_DisulfideDerivativeAtom (class in pyrosetta.rosetta.utility) vector1_core_scoring_dssp_Pairing (class in pyrosetta.rosetta.utility) vector1_core_scoring_dssp_StrandPairing (class in pyrosetta.rosetta.utility) vector1_core_scoring_EMapVector (class in pyrosetta.rosetta.utility) vector1_core_scoring_epr_deer_EPRSpinLabel (class in pyrosetta.rosetta.utility) vector1_core_scoring_etable_EtableParamsOnePair (class in pyrosetta.rosetta.utility) vector1_core_scoring_etable_etrie_GenericResidueConnectionData (class in pyrosetta.rosetta.utility) vector1_core_scoring_fiber_diffraction_OneGaussianScattering (class in pyrosetta.rosetta.utility) vector1_core_scoring_GenTorsionParams (class in pyrosetta.rosetta.utility) vector1_core_scoring_Hairpin (class in pyrosetta.rosetta.utility) vector1_core_scoring_hbonds_graph_HBondEdge (class in pyrosetta.rosetta.utility) vector1_core_scoring_hbonds_graph_HBondNode (class in pyrosetta.rosetta.utility) vector1_core_scoring_hbonds_HBEvalTuple (class in pyrosetta.rosetta.utility) vector1_core_scoring_hbonds_HBondWeightType (class in pyrosetta.rosetta.utility) vector1_core_scoring_loop_graph_Loop (class in pyrosetta.rosetta.utility) vector1_core_scoring_loop_graph_LoopCycle (class in pyrosetta.rosetta.utility) vector1_core_scoring_mhc_epitope_energy_AlleleMatrix (class in pyrosetta.rosetta.utility) vector1_core_scoring_motif_MotifHit (class in pyrosetta.rosetta.utility) vector1_core_scoring_motif_ResPairMotif (class in pyrosetta.rosetta.utility) vector1_core_scoring_motif_Xfres (class in pyrosetta.rosetta.utility) vector1_core_scoring_nmr_pcs_PCSSingle (class in pyrosetta.rosetta.utility) vector1_core_scoring_nmr_pre_PRESingle (class in pyrosetta.rosetta.utility) vector1_core_scoring_nmr_rdc_RDCSingle (class in pyrosetta.rosetta.utility) vector1_core_scoring_packing_Ball (class in pyrosetta.rosetta.utility) vector1_core_scoring_packstat_CavityBall (class in pyrosetta.rosetta.utility) vector1_core_scoring_packstat_CavityBallCluster (class in pyrosetta.rosetta.utility) vector1_core_scoring_packstat_LR_AtomData (class in pyrosetta.rosetta.utility) vector1_core_scoring_packstat_LR_MP_AtomData (class in pyrosetta.rosetta.utility) vector1_core_scoring_packstat_SimplePDB_Atom (class in pyrosetta.rosetta.utility) vector1_core_scoring_packstat_Sphere (class in pyrosetta.rosetta.utility) vector1_core_scoring_power_diagram_SAnode (class in pyrosetta.rosetta.utility) vector1_core_scoring_RDC (class in pyrosetta.rosetta.utility) vector1_core_scoring_RDC_Rohl (class in pyrosetta.rosetta.utility) vector1_core_scoring_rna_RNA_Motif (class in pyrosetta.rosetta.utility) vector1_core_scoring_ScoreType (class in pyrosetta.rosetta.utility) vector1_core_scoring_SmallAtNb (class in pyrosetta.rosetta.utility) vector1_core_scoring_SmoothScoreTermCoeffs (class in pyrosetta.rosetta.utility) vector1_core_scoring_SpringParams (class in pyrosetta.rosetta.utility) vector1_core_scoring_tableID (class in pyrosetta.rosetta.utility) vector1_core_select_residue_selector_ResidueRange (class in pyrosetta.rosetta.utility) vector1_core_sequence_Line (class in pyrosetta.rosetta.utility) vector1_core_sequence_SequenceAlignment (class in pyrosetta.rosetta.utility) vector1_double (class in pyrosetta.rosetta.utility) vector1_float (class in pyrosetta.rosetta.utility) vector1_int (class in pyrosetta.rosetta.utility) vector1_long (class in pyrosetta.rosetta.utility) vector1_numeric_CubicPolynomial (class in pyrosetta.rosetta.utility) vector1_numeric_geometry_hashing_Ball (class in pyrosetta.rosetta.utility) vector1_numeric_histograms_TwoDHistogram_unsigned_long_long_t (class in pyrosetta.rosetta.utility) vector1_numeric_HomogeneousTransform_double_t (class in pyrosetta.rosetta.utility) vector1_numeric_interpolation_spline_BicubicSpline (class in pyrosetta.rosetta.utility) vector1_numeric_interpolation_spline_CubicSpline (class in pyrosetta.rosetta.utility) vector1_numeric_interpolation_spline_interp_range (class in pyrosetta.rosetta.utility) vector1_numeric_interpolation_spline_Point (class in pyrosetta.rosetta.utility) vector1_numeric_MultiDimensionalHistogram (class in pyrosetta.rosetta.utility) vector1_numeric_random_WeightedSampler (class in pyrosetta.rosetta.utility) vector1_numeric_RocPoint (class in pyrosetta.rosetta.utility) vector1_numeric_urs_Quat (class in pyrosetta.rosetta.utility) vector1_numeric_xyzMatrix_double_t (class in pyrosetta.rosetta.utility) vector1_numeric_xyzTransform_double_t (class in pyrosetta.rosetta.utility) vector1_numeric_xyzVector_double_t (class in pyrosetta.rosetta.utility) vector1_numeric_xyzVector_float_t (class in pyrosetta.rosetta.utility) vector1_ObjexxFCL_FArray1D_double_t (class in pyrosetta.rosetta.utility) vector1_ObjexxFCL_FArray2D_double_t (class in pyrosetta.rosetta.utility) vector1_ObjexxFCL_FArray2D_numeric_xyzVector_double_t (class in pyrosetta.rosetta.utility) vector1_protocols_abinitio_AlternativePairings (class in pyrosetta.rosetta.utility) vector1_protocols_abinitio_ClassicAbinitio_StageID (class in pyrosetta.rosetta.utility) vector1_protocols_abinitio_PairingStatEntry (class in pyrosetta.rosetta.utility) vector1_protocols_abinitio_StageID (class in pyrosetta.rosetta.utility) vector1_protocols_antibody_AntibodyNumberingSchemeEnum (class in pyrosetta.rosetta.utility) vector1_protocols_antibody_CDRDefinitionEnum (class in pyrosetta.rosetta.utility) vector1_protocols_antibody_CDRNameEnum (class in pyrosetta.rosetta.utility) vector1_protocols_antibody_clusters_CDRClusterEnum (class in pyrosetta.rosetta.utility) vector1_protocols_antibody_clusters_ClusterData (class in pyrosetta.rosetta.utility) vector1_protocols_antibody_design_PDBNumbering (class in pyrosetta.rosetta.utility) vector1_protocols_backbone_moves_local_backbone_mover_Residue (class in pyrosetta.rosetta.utility) vector1_protocols_backrub_BackrubSegment (class in pyrosetta.rosetta.utility) vector1_protocols_branch_angle_BranchCoef1 (class in pyrosetta.rosetta.utility) vector1_protocols_branch_angle_BranchCoef2 (class in pyrosetta.rosetta.utility) vector1_protocols_canonical_sampling_DbTrajectoryRecorder_Frame (class in pyrosetta.rosetta.utility) vector1_protocols_canonical_sampling_TorsionSpec (class in pyrosetta.rosetta.utility) vector1_protocols_cartesian_CartesianAtom (class in pyrosetta.rosetta.utility) vector1_protocols_cartesian_MD_Angle (class in pyrosetta.rosetta.utility) vector1_protocols_cartesian_MD_Bond (class in pyrosetta.rosetta.utility) vector1_protocols_cartesian_MD_HarmonicDihedral (class in pyrosetta.rosetta.utility) vector1_protocols_cluster_DataPoint (class in pyrosetta.rosetta.utility) vector1_protocols_cluster_Exemplar (class in pyrosetta.rosetta.utility) vector1_protocols_constraints_additional_ConstraintEvaluator (class in pyrosetta.rosetta.utility) vector1_protocols_contact_map_Contact (class in pyrosetta.rosetta.utility) vector1_protocols_cyclic_peptide_PSM_StubMode (class in pyrosetta.rosetta.utility) vector1_protocols_denovo_design_components_BondInfo (class in pyrosetta.rosetta.utility) vector1_protocols_denovo_design_components_NamedSolution (class in pyrosetta.rosetta.utility) vector1_protocols_denovo_design_components_StructureSlice (class in pyrosetta.rosetta.utility) vector1_protocols_features_TaskOperationFeatures_Taskop_id_name_factory_ (class in pyrosetta.rosetta.utility) vector1_protocols_fold_from_loops_utils_NubSegment (class in pyrosetta.rosetta.utility) vector1_protocols_forge_build_Interval (class in pyrosetta.rosetta.utility) vector1_protocols_frag_picker_LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareTotalScore_t (class in pyrosetta.rosetta.utility) vector1_protocols_helical_bundle_BPC_Parameters (class in pyrosetta.rosetta.utility) vector1_protocols_hotspot_hashing_VectorPair (class in pyrosetta.rosetta.utility) vector1_protocols_hybridization_detailedControlsTagSetting (class in pyrosetta.rosetta.utility) vector1_protocols_indexed_structure_store_BackboneStub (class in pyrosetta.rosetta.utility) vector1_protocols_jd2_archive_Batch (class in pyrosetta.rosetta.utility) vector1_protocols_jd3_chunk_library_ChunkLibraryPreliminaryLarvalJob (class in pyrosetta.rosetta.utility) vector1_protocols_jd3_dag_node_managers_ResultElements (class in pyrosetta.rosetta.utility) vector1_protocols_jd3_full_model_FullModelPreliminaryLarvalJob (class in pyrosetta.rosetta.utility) vector1_protocols_jd3_standard_PreliminaryLarvalJob (class in pyrosetta.rosetta.utility) vector1_protocols_jumping_DisulfPairing (class in pyrosetta.rosetta.utility) vector1_protocols_jumping_JumpSelector_JumpWeightDef (class in pyrosetta.rosetta.utility) vector1_protocols_jumping_JumpSetup_JumpDef (class in pyrosetta.rosetta.utility) vector1_protocols_jumping_ResiduePairJumpSetup_JumpDef (class in pyrosetta.rosetta.utility) vector1_protocols_legacy_sewing_SewAtom (class in pyrosetta.rosetta.utility) vector1_protocols_legacy_sewing_SewResidue (class in pyrosetta.rosetta.utility) vector1_protocols_legacy_sewing_SewSegment (class in pyrosetta.rosetta.utility) vector1_protocols_ligand_docking_ga_ligand_dock_AtomProperties (class in pyrosetta.rosetta.utility) vector1_protocols_ligand_docking_ga_ligand_dock_GADockStageParams (class in pyrosetta.rosetta.utility) vector1_protocols_ligand_docking_ga_ligand_dock_Pharmacophore (class in pyrosetta.rosetta.utility) vector1_protocols_ligand_docking_ga_ligand_dock_ReweightableRepEnergy (class in pyrosetta.rosetta.utility) vector1_protocols_ligand_docking_ga_ligand_dock_TorsionDistrParams (class in pyrosetta.rosetta.utility) vector1_protocols_ligand_docking_ga_ligand_dock_TorsionType (class in pyrosetta.rosetta.utility) vector1_protocols_ligand_docking_ligand_options_InterfaceInfo (class in pyrosetta.rosetta.utility) vector1_protocols_ligand_docking_ProtLigPair_info (class in pyrosetta.rosetta.utility) vector1_protocols_loop_grower_LoopPartialSolution (class in pyrosetta.rosetta.utility) vector1_protocols_loop_grower_LoopPartialSolutionStore (class in pyrosetta.rosetta.utility) vector1_protocols_loop_grower_ResTorsions (class in pyrosetta.rosetta.utility) vector1_protocols_loop_grower_SheetPositions (class in pyrosetta.rosetta.utility) vector1_protocols_loops_Loop (class in pyrosetta.rosetta.utility) vector1_protocols_loops_LoopFromFileData (class in pyrosetta.rosetta.utility) vector1_protocols_loops_Loops (class in pyrosetta.rosetta.utility) vector1_protocols_loops_SerializedLoop (class in pyrosetta.rosetta.utility) vector1_protocols_make_rot_lib_CentroidRotNum (class in pyrosetta.rosetta.utility) vector1_protocols_make_rot_lib_RotData (class in pyrosetta.rosetta.utility) vector1_protocols_make_rot_lib_TorsionRange (class in pyrosetta.rosetta.utility) vector1_protocols_match_Hit (class in pyrosetta.rosetta.utility) vector1_protocols_match_match_dspos1 (class in pyrosetta.rosetta.utility) vector1_protocols_match_ProbeRadius (class in pyrosetta.rosetta.utility) vector1_protocols_match_upstream_BuildSet (class in pyrosetta.rosetta.utility) vector1_protocols_match_upstream_hit (class in pyrosetta.rosetta.utility) vector1_protocols_match_upstream_SampleStrategyData (class in pyrosetta.rosetta.utility) vector1_protocols_md_Constraint (class in pyrosetta.rosetta.utility) vector1_protocols_md_MDscheduleData (class in pyrosetta.rosetta.utility) vector1_protocols_mean_field_AAMatrix (class in pyrosetta.rosetta.utility) vector1_protocols_mean_field_jagged_array_double_std_allocator_double_t (class in pyrosetta.rosetta.utility) vector1_protocols_mean_field_RotMatrix (class in pyrosetta.rosetta.utility) vector1_protocols_membrane_SpanInfo (class in pyrosetta.rosetta.utility) vector1_protocols_monte_carlo_AcceptedScores (class in pyrosetta.rosetta.utility) vector1_protocols_motif_grafting_movers_motif2scaffold_indexes (class in pyrosetta.rosetta.utility) vector1_protocols_moves_TrialCounter (class in pyrosetta.rosetta.utility) vector1_protocols_mpi_refinement_MethodParams (class in pyrosetta.rosetta.utility) vector1_protocols_multistate_design_SingleStateEntityData (class in pyrosetta.rosetta.utility) vector1_protocols_nonlocal_Chunk (class in pyrosetta.rosetta.utility) vector1_protocols_optimize_weights_WeightRangeConstraint (class in pyrosetta.rosetta.utility) vector1_protocols_pack_daemon_StructureFileNames (class in pyrosetta.rosetta.utility) vector1_protocols_pdbinfo_manipulations_SequenceSpecification (class in pyrosetta.rosetta.utility) vector1_protocols_pmut_scan_Mutant (class in pyrosetta.rosetta.utility) vector1_protocols_pmut_scan_MutationData (class in pyrosetta.rosetta.utility) vector1_protocols_pose_creation_MergePDBMover_Overlap (class in pyrosetta.rosetta.utility) vector1_protocols_pose_creation_SliceToMiniProteinMover_Chunk (class in pyrosetta.rosetta.utility) vector1_protocols_pose_metric_calculators_EnergiesData (class in pyrosetta.rosetta.utility) vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_mutt (class in pyrosetta.rosetta.utility) vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_tm_region (class in pyrosetta.rosetta.utility) vector1_protocols_protein_interface_design_movers_VLBInstruction (class in pyrosetta.rosetta.utility) vector1_protocols_protein_interface_design_Transformation (class in pyrosetta.rosetta.utility) vector1_protocols_qsar_ColorGradient (class in pyrosetta.rosetta.utility) vector1_protocols_rbsegment_relax_RBResidueRange (class in pyrosetta.rosetta.utility) vector1_protocols_rbsegment_relax_RBSegment (class in pyrosetta.rosetta.utility) vector1_protocols_recces_Histogram (class in pyrosetta.rosetta.utility) vector1_protocols_relax_DatabaseRelaxScript (class in pyrosetta.rosetta.utility) vector1_protocols_rigid_Partner (class in pyrosetta.rosetta.utility) vector1_protocols_rosetta_scripts_ParsedProtocol_ParsedProtocolStep (class in pyrosetta.rosetta.utility) vector1_protocols_scoring_methods_pcs2_PcsDataCenter (class in pyrosetta.rosetta.utility) vector1_protocols_scoring_methods_pcs2_PcsDataLanthanide (class in pyrosetta.rosetta.utility) vector1_protocols_scoring_methods_pcs2_PcsEnergyParameter (class in pyrosetta.rosetta.utility) vector1_protocols_scoring_methods_pcs2_PcsGridSearchParameter (class in pyrosetta.rosetta.utility) vector1_protocols_scoring_methods_pcs2_PcsInputLine (class in pyrosetta.rosetta.utility) vector1_protocols_scoring_methods_pcs_PCS_data_per_lanthanides (class in pyrosetta.rosetta.utility) vector1_protocols_scoring_methods_pcs_PCS_line_data (class in pyrosetta.rosetta.utility) vector1_protocols_scoring_methods_pcsTs1_PCS_data_per_lanthanides_Ts1 (class in pyrosetta.rosetta.utility) vector1_protocols_scoring_methods_pcsTs1_PCS_line_data_Ts1 (class in pyrosetta.rosetta.utility) vector1_protocols_scoring_methods_pcsTs2_PCS_data_per_lanthanides_Ts2 (class in pyrosetta.rosetta.utility) vector1_protocols_scoring_methods_pcsTs2_PCS_line_data_Ts2 (class in pyrosetta.rosetta.utility) vector1_protocols_scoring_methods_pcsTs3_PCS_data_per_lanthanides_Ts3 (class in pyrosetta.rosetta.utility) vector1_protocols_scoring_methods_pcsTs3_PCS_line_data_Ts3 (class in pyrosetta.rosetta.utility) vector1_protocols_scoring_methods_pcsTs4_PCS_data_per_lanthanides_Ts4 (class in pyrosetta.rosetta.utility) vector1_protocols_scoring_methods_pcsTs4_PCS_line_data_Ts4 (class in pyrosetta.rosetta.utility) vector1_protocols_seeded_abinitio_SegmentSpec (class in pyrosetta.rosetta.utility) vector1_protocols_sewing_data_storage_ContactDescription (class in pyrosetta.rosetta.utility) vector1_protocols_sewing_data_storage_LigandDescription (class in pyrosetta.rosetta.utility) vector1_protocols_simple_filters_Quat (class in pyrosetta.rosetta.utility) vector1_protocols_simple_filters_RegionalConnections (class in pyrosetta.rosetta.utility) vector1_protocols_simple_filters_ResidueDepthFrag (class in pyrosetta.rosetta.utility) vector1_protocols_simple_moves_IonizableResidue (class in pyrosetta.rosetta.utility) vector1_protocols_simple_moves_LoggedFragmentMover_Item (class in pyrosetta.rosetta.utility) vector1_protocols_simple_moves_TorsionPerturbType (class in pyrosetta.rosetta.utility) vector1_protocols_simple_moves_WaterRot (class in pyrosetta.rosetta.utility) vector1_protocols_splice_BBDofs (class in pyrosetta.rosetta.utility) vector1_protocols_splice_ResidueBBDofs (class in pyrosetta.rosetta.utility) vector1_protocols_stepwise_modeler_protein_MainChainTorsionSet (class in pyrosetta.rosetta.utility) vector1_protocols_stepwise_modeler_rna_Combine_Tags_Info (class in pyrosetta.rosetta.utility) vector1_protocols_stepwise_modeler_rna_phosphate_PhosphateMove (class in pyrosetta.rosetta.utility) vector1_protocols_stepwise_monte_carlo_mover_Attachment (class in pyrosetta.rosetta.utility) vector1_protocols_stepwise_monte_carlo_mover_StepWiseMove (class in pyrosetta.rosetta.utility) vector1_protocols_stepwise_sampler_copy_dofs_ResidueAlternativeSet (class in pyrosetta.rosetta.utility) vector1_protocols_toolbox_match_enzdes_util_CstResInteractions (class in pyrosetta.rosetta.utility) vector1_protocols_toolbox_match_enzdes_util_ExternalGeomSampler (class in pyrosetta.rosetta.utility) vector1_protocols_toolbox_match_enzdes_util_ResInteractions (class in pyrosetta.rosetta.utility) vector1_protocols_toolbox_match_enzdes_util_SingleConstraint (class in pyrosetta.rosetta.utility) vector1_protocols_toolbox_ScoreRmsPoint (class in pyrosetta.rosetta.utility) vector1_protocols_trajectory_DbTrajectoryWriter_Frame (class in pyrosetta.rosetta.utility) vector1_short (class in pyrosetta.rosetta.utility) vector1_signed_char (class in pyrosetta.rosetta.utility) vector1_std__Rb_tree_const_iterator_protocols_match_downstream_hit_t (class in pyrosetta.rosetta.utility) vector1_std__Rb_tree_const_iterator_protocols_match_upstream_hit_t (class in pyrosetta.rosetta.utility) vector1_std_array_int_3_t (class in pyrosetta.rosetta.utility) vector1_std_list_std_pair_std_shared_ptr_const_protocols_match_downstream_SecMatchResiduePairEvaluator_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_std_list_std_pair_unsigned_long_std_shared_ptr_const_numeric_expression_parser_Expression_t (class in pyrosetta.rosetta.utility) vector1_std_list_std_pair_unsigned_long_std_shared_ptr_protocols_pack_daemon_NPDPropCalculator_t (class in pyrosetta.rosetta.utility) vector1_std_list_std_pair_unsigned_long_std_string_t (class in pyrosetta.rosetta.utility) vector1_std_list_std_shared_ptr_const_core_pack_task_ResfileCommand_t (class in pyrosetta.rosetta.utility) vector1_std_list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t (class in pyrosetta.rosetta.utility) vector1_std_list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t (class in pyrosetta.rosetta.utility) vector1_std_list_std_string_t (class in pyrosetta.rosetta.utility) vector1_std_list_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t (class in pyrosetta.rosetta.utility) vector1_std_map_core_chemical_AA_utility_vector1_double_std_allocator_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.utility) vector1_std_map_protocols_jumping_cstType_unsigned_long_std_less_protocols_jumping_cstType_std_allocator_std_pair_const_protocols_jumping_cstType_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_std_map_protocols_jumping_dofType_unsigned_long_std_less_protocols_jumping_dofType_std_allocator_std_pair_const_protocols_jumping_dofType_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_std_map_std_shared_ptr_const_core_conformation_Residue_double_std_less_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_pair_const_std_shared_ptr_const_core_conformation_Residue_double_t (class in pyrosetta.rosetta.utility) vector1_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t (class in pyrosetta.rosetta.utility) vector1_std_map_std_string_core_id_NamedAtomID_std_less_std_string_std_allocator_std_pair_const_std_string_core_id_NamedAtomID_t (class in pyrosetta.rosetta.utility) vector1_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t (class in pyrosetta.rosetta.utility) vector1_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t (class in pyrosetta.rosetta.utility) vector1_std_map_std_string_numeric_xyzVector_double_std_less_std_string_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t (class in pyrosetta.rosetta.utility) vector1_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t (class in pyrosetta.rosetta.utility) vector1_std_map_std_string_unsigned_long_std_less_std_string_std_allocator_std_pair_const_std_string_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_std_map_unsigned_long_core_chemical_AA_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_core_chemical_AA_t (class in pyrosetta.rosetta.utility) vector1_std_map_unsigned_long_std_list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t (class in pyrosetta.rosetta.utility) vector1_std_map_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_t (class in pyrosetta.rosetta.utility) vector1_std_map_unsigned_long_std_shared_ptr_protocols_frag_picker_CandidatesCollector_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_frag_picker_CandidatesCollector_t (class in pyrosetta.rosetta.utility) vector1_std_map_unsigned_long_unsigned_long_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_std_map_utility_keys_Key2Tuple_unsigned_long_unsigned_long_unsigned_long_std_less_utility_keys_Key2Tuple_unsigned_long_unsigned_long_std_allocator_std_pair_const_utility_keys_Key2Tuple_unsigned_long_unsigned_long_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_std_map_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_unsigned_long_std_less_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_std_allocator_std_pair_const_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_std_pair_bool_bool_t (class in pyrosetta.rosetta.utility) vector1_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.utility) vector1_std_pair_core_id_AtomID_core_id_AtomID_t (class in pyrosetta.rosetta.utility) vector1_std_pair_core_id_AtomID_core_kinematics_Jump_t (class in pyrosetta.rosetta.utility) vector1_std_pair_core_id_AtomID_double_t (class in pyrosetta.rosetta.utility) vector1_std_pair_core_id_AtomID_numeric_xyzVector_double_t (class in pyrosetta.rosetta.utility) vector1_std_pair_core_id_AtomID_std_pair_core_id_AtomID_core_id_AtomID_t (class in pyrosetta.rosetta.utility) vector1_std_pair_core_id_DOF_ID_double_t (class in pyrosetta.rosetta.utility) vector1_std_pair_core_id_NamedAtomID_core_id_NamedAtomID_t (class in pyrosetta.rosetta.utility) vector1_std_pair_core_id_TorsionID_core_id_TorsionID_t (class in pyrosetta.rosetta.utility) vector1_std_pair_core_id_TorsionID_std_string_t (class in pyrosetta.rosetta.utility) vector1_std_pair_core_io_HeaderInformation_CompoundToken_std_string_t (class in pyrosetta.rosetta.utility) vector1_std_pair_core_io_raw_data_DisulfideFile_ResNum_core_io_raw_data_DisulfideFile_ResNum_t (class in pyrosetta.rosetta.utility) vector1_std_pair_core_scoring_aa_composition_energy_TailFunction_core_scoring_aa_composition_energy_TailFunction_t (class in pyrosetta.rosetta.utility) vector1_std_pair_core_scoring_disulfides_CentroidDisulfideEnergyComponents_bool_t (class in pyrosetta.rosetta.utility) vector1_std_pair_core_scoring_disulfides_DisulfideMatchingEnergyComponents_bool_t (class in pyrosetta.rosetta.utility) vector1_std_pair_core_scoring_disulfides_FullatomDisulfideEnergyComponents_bool_t (class in pyrosetta.rosetta.utility) vector1_std_pair_double_double_t (class in pyrosetta.rosetta.utility) vector1_std_pair_double_numeric_xyzVector_double_t (class in pyrosetta.rosetta.utility) vector1_std_pair_double_std_string_t (class in pyrosetta.rosetta.utility) vector1_std_pair_double_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_std_pair_double_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.utility) vector1_std_pair_int_int_t (class in pyrosetta.rosetta.utility) vector1_std_pair_int_std_shared_ptr_const_core_conformation_ResidueMatcher_t (class in pyrosetta.rosetta.utility) vector1_std_pair_int_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_std_pair_long_long_t (class in pyrosetta.rosetta.utility) vector1_std_pair_numeric_xyzVector_double_double_t (class in pyrosetta.rosetta.utility) vector1_std_pair_numeric_xyzVector_double_numeric_xyzVector_double_t (class in pyrosetta.rosetta.utility) vector1_std_pair_numeric_xyzVector_float_int_t (class in pyrosetta.rosetta.utility) vector1_std_pair_protocols_forge_build_Interval_std_string_t (class in pyrosetta.rosetta.utility) vector1_std_pair_protocols_loophash_BackboneSegment_std_string_t (class in pyrosetta.rosetta.utility) vector1_std_pair_protocols_sewing_data_storage_Basis_protocols_sewing_data_storage_Basis_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_list_std_shared_ptr_const_core_conformation_Residue_utility_vector1_std_shared_ptr_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_std_allocator_std_shared_ptr_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_pair_unsigned_long_unsigned_long_std_pair_unsigned_long_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_set_unsigned_long_std_set_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_shared_ptr_const_core_pose_ResidueIndexDescription_std_shared_ptr_const_core_pose_ResidueIndexDescription_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_shared_ptr_const_numeric_expression_parser_Expression_std_shared_ptr_protocols_pack_daemon_SurrogateVariableExpression_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_shared_ptr_core_io_silent_SilentStruct_utility_file_FileName_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_shared_ptr_protocols_calc_taskop_movers_DesignRepackMover_bool_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_shared_ptr_protocols_calc_taskop_movers_DesignRepackMover_double_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_shared_ptr_protocols_filters_Filter_double_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_shared_ptr_protocols_genetic_algorithm_Entity_std_pair_utility_vector1_double_std_allocator_double_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_shared_ptr_protocols_hotspot_hashing_HotspotStubSet_std_pair_std_shared_ptr_protocols_hotspot_hashing_HotspotStub_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_shared_ptr_protocols_jd3_InnerLarvalJob_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_shared_ptr_protocols_jd3_JobSummary_std_shared_ptr_protocols_jd3_JobResult_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_string_bool_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_string_core_kinematics_Jump_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_string_double_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_string_protocols_ligand_docking_Translate_info_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_string_std_shared_ptr_const_core_chemical_ResidueType_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_string_std_shared_ptr_const_protocols_qsar_scoring_grid_GridSet_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_string_std_string_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_string_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_std_pair_std_vector_unsigned_long_double_t (class in pyrosetta.rosetta.utility) vector1_std_pair_unsigned_long_bool_t (class in pyrosetta.rosetta.utility) vector1_std_pair_unsigned_long_double_t (class in pyrosetta.rosetta.utility) vector1_std_pair_unsigned_long_protocols_ligand_docking_ga_ligand_dock_Pharmacophore_t (class in pyrosetta.rosetta.utility) vector1_std_pair_unsigned_long_protocols_sic_dock_Vec3_t (class in pyrosetta.rosetta.utility) vector1_std_pair_unsigned_long_std_pair_core_chemical_AA_core_chemical_AA_t (class in pyrosetta.rosetta.utility) vector1_std_pair_unsigned_long_std_pair_unsigned_long_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_std_pair_unsigned_long_std_shared_ptr_const_numeric_expression_parser_Expression_t (class in pyrosetta.rosetta.utility) vector1_std_pair_unsigned_long_std_shared_ptr_const_protocols_pack_daemon_PackDaemon_t (class in pyrosetta.rosetta.utility) vector1_std_pair_unsigned_long_std_shared_ptr_const_utility_tag_Tag_t (class in pyrosetta.rosetta.utility) vector1_std_pair_unsigned_long_std_shared_ptr_protocols_helical_bundle_BundleParametrizationCalculator_t (class in pyrosetta.rosetta.utility) vector1_std_pair_unsigned_long_std_shared_ptr_protocols_pack_daemon_PackDaemon_t (class in pyrosetta.rosetta.utility) vector1_std_pair_unsigned_long_std_string_t (class in pyrosetta.rosetta.utility) vector1_std_pair_unsigned_long_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_std_pair_unsigned_long_utility_vector1_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_std_allocator_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.utility) vector1_std_pair_utility_fixedsizearray1_unsigned_long_2_std_shared_ptr_const_core_scoring_methods_CartBondedParameters_t (class in pyrosetta.rosetta.utility) vector1_std_pair_utility_fixedsizearray1_unsigned_long_3_std_shared_ptr_const_core_scoring_methods_CartBondedParameters_t (class in pyrosetta.rosetta.utility) vector1_std_pair_utility_fixedsizearray1_unsigned_long_3_std_string_t (class in pyrosetta.rosetta.utility) vector1_std_pair_utility_fixedsizearray1_unsigned_long_4_std_shared_ptr_const_core_scoring_methods_CartBondedParameters_t (class in pyrosetta.rosetta.utility) vector1_std_pair_utility_fixedsizearray1_unsigned_long_4_std_string_t (class in pyrosetta.rosetta.utility) vector1_std_pair_utility_fixedsizearray1_unsigned_long_5_std_string_t (class in pyrosetta.rosetta.utility) vector1_std_pair_utility_fixedsizearray1_unsigned_long_6_std_string_t (class in pyrosetta.rosetta.utility) vector1_std_pair_utility_vector1_std_pair_double_std_shared_ptr_const_core_pack_guidance_scoreterms_sap_SapConstraintHelper_std_allocator_std_pair_double_std_shared_ptr_const_core_pack_guidance_scoreterms_sap_SapConstraintHelper_std_shared_ptr_const_core_pack_guidance_scoreterms_sap_SapMathConstraint_t (class in pyrosetta.rosetta.utility) vector1_std_pair_utility_vector1_unsigned_long_std_allocator_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_std_set_char_t (class in pyrosetta.rosetta.utility) vector1_std_set_core_id_NamedAtomID_t (class in pyrosetta.rosetta.utility) vector1_std_set_std_string_t (class in pyrosetta.rosetta.utility) vector1_std_set_unsigned_long_t (class in pyrosetta.rosetta.utility)

vector1_std_shared_ptr_basic_database_schema_generator_Constraint_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_basic_datacache_CacheableData_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_basic_citation_manager_Citation_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_basic_citation_manager_CitationCollectionBase_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_basic_citation_manager_UnpublishedModuleAuthor_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_chemical_Element_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_chemical_Metapatch_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_chemical_Patch_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_chemical_ResidueType_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_conformation_Residue_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_fragment_FragData_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_fragment_FragSet_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_fragment_Frame_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_pack_dunbrack_cenrot_SingleResidueCenrotLibrary_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_pack_rotamer_set_RotamerSet_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_pack_rotamers_SingleResidueRotamerLibrary_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_pack_task_TaskFactory_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_pose_Pose_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_scoring_aa_composition_energy_AACompositionEnergySetup_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_scoring_aa_composition_energy_SequenceConstraint_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_scoring_constraints_AngleConstraint_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_scoring_constraints_AtomPairConstraint_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_scoring_constraints_DihedralConstraint_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_scoring_dna_TorsionFourierComponent_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_scoring_hbonds_FadeInterval_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_scoring_hbonds_HBond_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_scoring_hbonds_Polynomial_1d_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_scoring_loop_graph_evaluator_LoopClosePotentialEvaluator_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_scoring_methods_LongRangeTwoBodyEnergy_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_scoring_methods_OneBodyEnergy_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_scoring_methods_TwoBodyEnergy_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_scoring_mhc_epitope_energy_MHCEpitopeEnergySetup_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_scoring_netcharge_energy_NetChargeEnergySetup_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_scoring_PDatom_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_scoring_ScoreFunction_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_core_simple_metrics_SimpleMetric_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_numeric_expression_parser_Expression_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_numeric_expression_parser_VariableExpression_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_abinitio_Template_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_chemistries_Chemistry_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_constraint_generator_ConstraintGenerator_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_denovo_design_architects_DeNovoArchitect_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_denovo_design_components_SegmentPairing_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_denovo_design_components_StructureData_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_denovo_design_connection_ConnectionArchitect_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_filters_Filter_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_genetic_algorithm_Entity_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_hbnet_HBondResStruct_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_jd3_InputSource_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_kinematic_closure_ClosureSolution_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_match_downstream_AtomGeometrySecMatchRPE_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_match_downstream_DownstreamBuilder_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_motifs_Motif_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_motifs_MotifHit_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_moves_RampingFunc_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_multistage_rosetta_scripts_cluster_ClusterMetric_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_pack_daemon_VectorExpression_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_sic_dock_RigidScore_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_simple_filters_ResidueDepthData_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_CovalentConnectionReplaceInfo_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintParameters_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_InvrotCollector_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_utility_libsvm_Svm_rosetta_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_const_utility_tag_Tag_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_chemical_AtomProperties_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_chemical_Element_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_chemical_gasteiger_GasteigerAtomTypeData_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_chemical_MMAtomType_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_chemical_MutableChiRecord_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_chemical_MutableResidueType_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_chemical_Orbital_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_chemical_orbitals_OrbitalType_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_chemical_PatchCase_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_chemical_PatchOperation_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_chemical_PoseResidueTypeSet_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_chemical_ResidueTypeSelectorSingle_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_chemical_rings_RingConformerSet_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_chemical_sdf_MolFileIOMolecule_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_conformation_AbstractRotamerTrie_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_conformation_membrane_Span_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_conformation_orbitals_OrbitalXYZCoords_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_conformation_parametric_Parameter_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_conformation_parametric_Parameters_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_conformation_parametric_ParametersSet_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_conformation_Residue_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_conformation_UltraLightResidue_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_energy_methods_ScoreCache_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_environment_FoldTreeSketch_Node_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_environment_LocalPosition_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_fragment_FragData_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_fragment_FragSet_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_fragment_Frame_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_fragment_picking_old_vall_eval_VallFragmentEval_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_fragment_picking_old_vall_gen_VallFragmentGen_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_fragment_SingleResidueFragData_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_import_pose_libraries_ChunkSet_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_import_pose_pose_stream_PoseInputStream_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_io_silent_SilentStruct_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_kinematics_AtomTree_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_kinematics_jacobian_ModuleType1_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_kinematics_jacobian_SeriesJacobians_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_kinematics_tree_Atom_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_optimization_DOF_Node_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_optimization_NumDerivCheckData_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_pack_guidance_scoreterms_sap_SapConstraintHelper_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_pack_interaction_graph_NPDHBond_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_pack_rotamer_set_RotamerSet_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_pack_rotamer_set_WaterAnchorInfo_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_pack_scmin_ResidueAtomTreeCollection_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_pack_task_IGEdgeReweighter_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_pack_task_operation_OperateOnResidueSubset_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_pack_task_operation_ResFilter_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_pack_task_PackerTask_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_pack_task_ResfileCommand_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_pose_datacache_CacheableObserver_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_pose_full_model_info_SubMotifInfo_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_pose_MiniPose_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_pose_Pose_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_aa_composition_energy_AACompositionEnergySetup_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_aa_composition_energy_AACompositionPropertiesSet_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_bin_transitions_BinTransitionData_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_constraints_Constraint_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_constraints_DOF_Constraint_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_constraints_Obsolet_NamedAtomPairConstraint_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_constraints_ResidueConstraints_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_ContextGraph_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_facts_FACTSResidueInfo_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_func_AmberPeriodicFunc_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_func_Func_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_GenBornResidueInfo_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_hbonds_HBond_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_lkball_LKB_ResidueInfo_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_LREnergyContainer_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_methods_ContextDependentLRTwoBodyEnergy_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_methods_ContextDependentOneBodyEnergy_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_methods_ContextDependentTwoBodyEnergy_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_methods_ContextIndependentLRTwoBodyEnergy_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_methods_ContextIndependentOneBodyEnergy_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_methods_ContextIndependentTwoBodyEnergy_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_methods_EnergyMethodCreator_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_methods_TwoBodyEnergy_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_methods_WholeStructureEnergy_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_mhc_epitope_energy_MHCEpitopeEnergySetup_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_MultipoleElecResidueInfo_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_MultipoleParameter_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_netcharge_energy_NetChargeEnergySetup_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_nmr_NMRDummySpinlabelConformer_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_nmr_pcs_PCSMultiSet_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_nmr_pcs_PCSSingle_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_nmr_pcs_PCSSingleSet_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_nmr_pre_PREMultiSet_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_nmr_pre_PRESingleSet_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_nmr_rdc_RDCMultiSet_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_nmr_rdc_RDCSingleSet_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_PDatom_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_PDvertex_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_power_diagram_PDsphere_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_ResidualDipolarCoupling_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_saxs_DistanceHistogram_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_saxs_FormFactor_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_ScoreFunction_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_trie_RotamerTrieBase_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_scoring_VdWTinkerResidueInfo_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_sequence_Cell_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_sequence_ScoringScheme_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_core_sequence_Sequence_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_numeric_expression_parser_VariableExpression_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_numeric_interpolation_spline_Interpolator_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_numeric_kdtree_KDPoint_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_antibody_CDRSetOptions_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_antibody_clusters_CDRCluster_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_antibody_design_CDRGraftDesignOptions_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_antibody_design_CDRSeqDesignOptions_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_antibody_PDBLandmark_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_backbone_moves_local_backbone_mover_free_peptide_movers_FreePeptideMover_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_canonical_sampling_mc_convergence_checks_HPool_RMSD_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_canonical_sampling_ThermodynamicMover_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_canonical_sampling_ThermodynamicObserver_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_chemistries_Chemistry_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_denovo_design_architects_StrandArchitect_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_denovo_design_components_StructureDataPerturber_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_enzdes_EnzdesFlexibleRegion_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_evaluation_PoseEvaluator_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_features_FeaturesReporter_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_filters_CombinedFilter_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_filters_CompoundFilter_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_filters_Filter_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_fldsgn_topology_BetaAlphaBetaMotif_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_fldsgn_topology_Helix_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_fldsgn_topology_HelixPairing_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_fldsgn_topology_HSSTriplet_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_fldsgn_topology_Loop_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_fldsgn_topology_Sheet_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_fldsgn_topology_Strand_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_flxbb_DesignTask_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_forge_build_BuildInstruction_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_forge_remodel_RemodelConstraintGenerator_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_forge_remodel_ResidueVicinityInfo_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_frag_picker_Contact_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_frag_picker_FragmentSelectingRule_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_frag_picker_quota_ABEGO_SS_Map_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_frag_picker_quota_QuotaPool_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_frag_picker_scores_AdaptiveScoreHistogram_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreManager_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_frag_picker_scores_FragmentScoringMethod_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_frag_picker_VallChunk_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_frag_picker_VallChunkFilter_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_frag_picker_VallResidue_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_frags_SingleResidueTorsionFragmentLibrary_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_frags_TorsionFragment_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_generalized_kinematic_closure_filter_GeneralizedKICfilter_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_generalized_kinematic_closure_perturber_GeneralizedKICperturber_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_genetic_algorithm_Entity_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_helical_bundle_MakeBundleHelix_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_helical_bundle_predict_HBPHelix_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_jd3_chunk_library_ChunkLibraryInnerLarvalJob_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_jd3_dag_node_managers_NodeManager_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_jd3_full_model_FullModelInnerLarvalJob_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_jd3_InnerLarvalJob_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_jd3_output_OutputSpecification_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_jd3_output_ResultOutputter_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_jobdist_BasicJob_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_jumping_ResiduePairJump_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_jumping_ResiduePairJumpSingle_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_kinematic_closure_perturbers_Perturber_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_legacy_sewing_sampling_requirements_LegacyGlobalRequirement_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_ligand_docking_rdf_RDFBase_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_ligand_docking_ResidueTorsionRestraints_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_loop_modeling_LoopMover_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_loops_loop_mover_refine_LoopRefineInnerCycle_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_loops_Loops_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_match_Bool3DGrid_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_match_BumpGrid_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_match_output_BestMatchesCollection_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_match_output_DownstreamCoordinateKinemageWriter_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_match_upstream_ScaffoldBuildPoint_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_match_upstream_UpstreamBuilder_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_membrane_geometry_EmbeddingDef_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_metal_interface_MetalSiteResidue_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_motifs_BuildPosition_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_moves_MonteCarloExceptionConverge_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_moves_Mover_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_multistate_design_SingleState_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_noesy_assign_CrossPeak_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_noesy_assign_Resonance_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_optimize_weights_OptEPositionData_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_optimize_weights_PNatAAOptERotamerData_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_optimize_weights_PNatRotOptERotamerData_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_optimize_weights_SingleStructureData_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_peptide_deriver_PeptideDeriverOutputter_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_pose_length_moves_PossibleLoop_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_pose_sewing_data_storage_PoseWithTerminalSegmentsOfKnownDSSP_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_qsar_scoring_grid_SingleGrid_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_recces_sampler_MC_OneTorsion_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_recces_sampler_MC_Sampler_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_recces_sampler_rna_MC_RNA_Sugar_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_recces_sampler_rna_MC_RNA_Suite_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_rigid_RigidBodyPerturbMover_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_rigid_RigidBodySpinMover_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_rigid_RigidBodyTransMover_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_rosetta_scripts_PoseSelector_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_scoring_Interface_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_seeded_abinitio_GrowPeptidesSegment_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_sewing_data_storage_LigandContact_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_sewing_data_storage_SmartSegment_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_sewing_data_storage_SmartSewingResidue_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_sewing_requirements_AssemblyRequirement_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_sewing_scoring_AssemblyScorer_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_simple_filters_DeltaFilter_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_simple_moves_CopyDofMover_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_stepwise_modeler_protein_InputStreamWithResidueInfo_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_stepwise_modeler_protein_loop_close_StepWiseProteinCCD_Closer_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_stepwise_modeler_rna_checker_RNA_AtrRepChecker_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_stepwise_modeler_rna_checker_RNA_ChainClosableGeometryChecker_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_stepwise_modeler_rna_checker_RNA_ChainClosureChecker_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_stepwise_modeler_rna_sugar_SugarModeling_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_stepwise_sampler_copy_dofs_ResidueAlternativeSet_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_stepwise_sampler_copy_dofs_ResidueAlternativeStepWiseSampler_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_stepwise_sampler_StepWiseSampler_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_stepwise_sampler_StepWiseSamplerSized_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_stepwise_screener_StepWiseScreener_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_toolbox_KClusterElement_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_toolbox_match_enzdes_util_EnzConstraintParameters_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_toolbox_match_enzdes_util_EnzCstTemplateResCache_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_toolbox_match_enzdes_util_EnzdesCstParamCache_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_toolbox_match_enzdes_util_EnzdesLoopInfo_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_toolbox_match_enzdes_util_InvrotTarget_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_toolbox_match_enzdes_util_InvrotTreeNode_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_toolbox_match_enzdes_util_LigandConformer_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_toolbox_match_enzdes_util_MatchConstraintFileInfo_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_toolbox_match_enzdes_util_MatchConstraintFileInfoList_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_topology_broker_claims_JumpClaim_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_topology_broker_claims_SequenceClaim_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_topology_broker_TopologyClaimer_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_protocols_vardist_solaccess_VarSolDRotamerDots_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_std_unordered_set_std_string_std_hash_std_string_std_equal_to_std_string_std_allocator_std_string_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_utility_graph_UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t (class in pyrosetta.rosetta.utility) vector1_std_shared_ptr_utility_graph_UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t (class in pyrosetta.rosetta.utility) vector1_std_string (class in pyrosetta.rosetta.utility) vector1_std_tuple_double_double_t (class in pyrosetta.rosetta.utility) vector1_std_tuple_std_string_double_double_double_t (class in pyrosetta.rosetta.utility) vector1_std_unordered_map_std_pair_unsigned_long_unsigned_long_std_shared_ptr_const_protocols_multistage_rosetta_scripts_cluster_ClusterMetric_protocols_multistage_rosetta_scripts_JobResultID_hash_std_equal_to_std_pair_unsigned_long_unsigned_long_std_allocator_std_pair_const_std_pair_unsigned_long_unsigned_long_std_shared_ptr_const_protocols_multistage_rosetta_scripts_cluster_ClusterMetric_t (class in pyrosetta.rosetta.utility) vector1_std_vector_std_string_t (class in pyrosetta.rosetta.utility) vector1_std_weak_ptr_const_core_kinematics_AtomTree_t (class in pyrosetta.rosetta.utility) vector1_std_weak_ptr_const_protocols_forge_build_BuildInstruction_t (class in pyrosetta.rosetta.utility) vector1_std_weak_ptr_const_protocols_topology_broker_TopologyClaimer_t (class in pyrosetta.rosetta.utility) vector1_std_weak_ptr_protocols_jd3_JGJobNode_t (class in pyrosetta.rosetta.utility) vector1_std_weak_ptr_protocols_jd3_JGResultNode_t (class in pyrosetta.rosetta.utility) vector1_std_weak_ptr_protocols_noesy_assign_Resonance_t (class in pyrosetta.rosetta.utility) vector1_string (in module pyrosetta.rosetta.utility) vector1_unsigned_char (class in pyrosetta.rosetta.utility) vector1_unsigned_int (class in pyrosetta.rosetta.utility) vector1_unsigned_long (class in pyrosetta.rosetta.utility) vector1_unsigned_short (class in pyrosetta.rosetta.utility) vector1_utility_file_FileName (class in pyrosetta.rosetta.utility) vector1_utility_file_PathName (class in pyrosetta.rosetta.utility) vector1_utility_fixedsizearray1_double_2_t (class in pyrosetta.rosetta.utility) vector1_utility_fixedsizearray1_double_3_t (class in pyrosetta.rosetta.utility) vector1_utility_fixedsizearray1_double_4_t (class in pyrosetta.rosetta.utility) vector1_utility_fixedsizearray1_unsigned_long_3_t (class in pyrosetta.rosetta.utility) vector1_utility_fixedsizearray1_unsigned_long_7_t (class in pyrosetta.rosetta.utility) vector1_utility_graph_DS_Node (class in pyrosetta.rosetta.utility) vector1_utility_graph_UEEdge_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t (class in pyrosetta.rosetta.utility) vector1_utility_graph_UEEdge_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t (class in pyrosetta.rosetta.utility) vector1_utility_history_queue_struct (class in pyrosetta.rosetta.utility) vector1_utility_keys_Key2Tuple_double_double_t (class in pyrosetta.rosetta.utility) vector1_utility_keys_Key2Tuple_unsigned_long_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_utility_keys_Key3Tuple_protocols_loops_Loop_std_shared_ptr_core_kinematics_MoveMap_std_shared_ptr_core_kinematics_MoveMap_t (class in pyrosetta.rosetta.utility) vector1_utility_keys_Key3Tuple_unsigned_long_unsigned_long_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_utility_keys_Key4Tuple_unsigned_long_unsigned_long_unsigned_long_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_utility_options_BooleanOption (class in pyrosetta.rosetta.utility) vector1_utility_options_BooleanVectorOption (class in pyrosetta.rosetta.utility) vector1_utility_options_FileVectorOption (class in pyrosetta.rosetta.utility) vector1_utility_options_IntegerOption (class in pyrosetta.rosetta.utility) vector1_utility_options_IntegerVectorOption (class in pyrosetta.rosetta.utility) vector1_utility_options_OptionTypes (class in pyrosetta.rosetta.utility) vector1_utility_options_PathOption (class in pyrosetta.rosetta.utility) vector1_utility_options_PathVectorOption (class in pyrosetta.rosetta.utility) vector1_utility_options_RealOption (class in pyrosetta.rosetta.utility) vector1_utility_options_RealVectorOption (class in pyrosetta.rosetta.utility) vector1_utility_options_ResidueChainVectorOption (class in pyrosetta.rosetta.utility) vector1_utility_options_StringOption (class in pyrosetta.rosetta.utility) vector1_utility_options_StringVectorOption (class in pyrosetta.rosetta.utility) vector1_utility_options_VariantOption_utility_options_ScalarOption_t (class in pyrosetta.rosetta.utility) vector1_utility_options_VariantOption_utility_options_VectorOption_t (class in pyrosetta.rosetta.utility) vector1_utility_pointer_DeepCopyOP_protocols_antibody_design_CDRSeqDesignOptions_t (class in pyrosetta.rosetta.utility) vector1_utility_vector0_bool_std_allocator_bool_t (class in pyrosetta.rosetta.utility) vector1_utility_vector0_core_conformation_ppo_torsion_bin_std_allocator_core_conformation_ppo_torsion_bin_t (class in pyrosetta.rosetta.utility) vector1_utility_vector0_float_std_allocator_float_t (class in pyrosetta.rosetta.utility) vector1_utility_vector0_unsigned_short_std_allocator_unsigned_short_t (class in pyrosetta.rosetta.utility) vector1_utility_vector0_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_bool_std_allocator_bool_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_char_std_allocator_char_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_chemical_BondName_std_allocator_core_chemical_BondName_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_chemical_BondRingness_std_allocator_core_chemical_BondRingness_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_chemical_VariantType_std_allocator_core_chemical_VariantType_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_id_AtomID_std_allocator_core_id_AtomID_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_id_DOF_ID_std_allocator_core_id_DOF_ID_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_id_NamedAtomID_std_allocator_core_id_NamedAtomID_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_id_TorsionID_std_allocator_core_id_TorsionID_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_optimization_DerivCheckDataPoint_std_allocator_core_optimization_DerivCheckDataPoint_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_optimization_DOF_DataPoint_std_allocator_core_optimization_DOF_DataPoint_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_pack_dunbrack_DunbrackRotamerSampleData_std_allocator_core_pack_dunbrack_DunbrackRotamerSampleData_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_pack_interaction_graph_DotSphere_std_allocator_core_pack_interaction_graph_DotSphere_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_pose_Pose_std_allocator_core_pose_Pose_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_scoring_func_SOGFunc_Impl_std_allocator_core_scoring_func_SOGFunc_Impl_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_scoring_lkball_WaterBuilder_std_allocator_core_scoring_lkball_WaterBuilder_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_scoring_packstat_Circle__star__std_allocator_core_scoring_packstat_Circle__star__t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_scoring_packstat_LR_AtomData_std_allocator_core_scoring_packstat_LR_AtomData_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_scoring_packstat_LR_MP_AtomData_std_allocator_core_scoring_packstat_LR_MP_AtomData_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_scoring_power_diagram_PDsphere__star__std_allocator_core_scoring_power_diagram_PDsphere__star__t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_scoring_power_diagram_SAnode_std_allocator_core_scoring_power_diagram_SAnode_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_scoring_rna_chemical_shift_ChemicalShiftData_std_allocator_core_scoring_rna_chemical_shift_ChemicalShiftData_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_core_scoring_ScoreType_std_allocator_core_scoring_ScoreType_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_float_std_allocator_float_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_int_std_allocator_int_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_long_std_allocator_long_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_numeric_HomogeneousTransform_double_std_allocator_numeric_HomogeneousTransform_double_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_numeric_interpolation_spline_BicubicSpline_std_allocator_numeric_interpolation_spline_BicubicSpline_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_numeric_interpolation_spline_CubicSpline_std_allocator_numeric_interpolation_spline_CubicSpline_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_numeric_xyzVector_float_std_allocator_numeric_xyzVector_float_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_ObjexxFCL_ubyte_std_allocator_ObjexxFCL_ubyte_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_protocols_antibody_FrameWork_std_allocator_protocols_antibody_FrameWork_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_protocols_denovo_design_components_StrandOrientation_std_allocator_protocols_denovo_design_components_StrandOrientation_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_protocols_denovo_design_components_StructureSlice_std_allocator_protocols_denovo_design_components_StructureSlice_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_protocols_frag_picker_scores_GunnTuple_std_allocator_protocols_frag_picker_scores_GunnTuple_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_protocols_jd3_dag_node_managers_ResultElements_std_allocator_protocols_jd3_dag_node_managers_ResultElements_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_protocols_legacy_sewing_SewSegment_std_allocator_protocols_legacy_sewing_SewSegment_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_protocols_ligand_docking_ga_ligand_dock_PlaceableRotamer_std_allocator_protocols_ligand_docking_ga_ligand_dock_PlaceableRotamer_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_protocols_loops_Loops_std_allocator_protocols_loops_Loops_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_protocols_make_rot_lib_CentroidRotNum_std_allocator_protocols_make_rot_lib_CentroidRotNum_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_protocols_match_Hit_std_allocator_protocols_match_Hit_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_protocols_splice_ROT_std_allocator_protocols_splice_ROT_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_protocols_stepwise_legacy_modeler_rna_Cluster_Member_std_allocator_protocols_stepwise_legacy_modeler_rna_Cluster_Member_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_protocols_stepwise_modeler_protein_MainChainTorsionSet_std_allocator_protocols_stepwise_modeler_protein_MainChainTorsionSet_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_protocols_toolbox_match_enzdes_util_ExternalGeomSampler_std_allocator_protocols_toolbox_match_enzdes_util_ExternalGeomSampler_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_std_allocator_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_pair_int_int_std_allocator_std_pair_int_int_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_pair_numeric_xyzVector_double_numeric_xyzVector_double_std_allocator_std_pair_numeric_xyzVector_double_numeric_xyzVector_double_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_std_allocator_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_pair_std_string_std_string_std_allocator_std_pair_std_string_std_string_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_pair_unsigned_long_std_pair_std_pair_double_double_unsigned_long_std_allocator_std_pair_unsigned_long_std_pair_std_pair_double_double_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_pair_unsigned_long_unsigned_long_std_allocator_std_pair_unsigned_long_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_set_protocols_match_downstream_hit_std_less_protocols_match_downstream_hit_std_allocator_protocols_match_downstream_hit_std_allocator_std_set_protocols_match_downstream_hit_std_less_protocols_match_downstream_hit_std_allocator_protocols_match_downstream_hit_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_set_protocols_match_upstream_hit_std_less_protocols_match_upstream_hit_std_allocator_protocols_match_upstream_hit_std_allocator_std_set_protocols_match_upstream_hit_std_less_protocols_match_upstream_hit_std_allocator_protocols_match_upstream_hit_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_const_core_scoring_dna_TorsionFourierComponent_std_allocator_std_shared_ptr_const_core_scoring_dna_TorsionFourierComponent_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_std_allocator_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_const_protocols_match_upstream_ScaffoldBuildPoint_std_allocator_std_shared_ptr_const_protocols_match_upstream_ScaffoldBuildPoint_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_const_protocols_simple_filters_ResidueDepthData_std_allocator_std_shared_ptr_const_protocols_simple_filters_ResidueDepthData_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_core_conformation_Residue_std_allocator_std_shared_ptr_core_conformation_Residue_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_core_kinematics_tree_Atom_std_allocator_std_shared_ptr_core_kinematics_tree_Atom_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_core_optimization_DOF_Node_std_allocator_std_shared_ptr_core_optimization_DOF_Node_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_core_pack_interaction_graph_NPDHBond_std_allocator_std_shared_ptr_core_pack_interaction_graph_NPDHBond_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_core_pack_task_ResfileCommand_std_allocator_std_shared_ptr_core_pack_task_ResfileCommand_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_core_scoring_saxs_DistanceHistogram_std_allocator_std_shared_ptr_core_scoring_saxs_DistanceHistogram_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_core_sequence_Cell_std_allocator_std_shared_ptr_core_sequence_Cell_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_protocols_antibody_PDBLandmark_std_allocator_std_shared_ptr_protocols_antibody_PDBLandmark_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_protocols_fldsgn_topology_HelixPairing_std_allocator_std_shared_ptr_protocols_fldsgn_topology_HelixPairing_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_std_allocator_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_protocols_flexpack_rotamer_set_FlexbbRotamerSet_std_allocator_std_shared_ptr_protocols_flexpack_rotamer_set_FlexbbRotamerSet_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_quota_QuotaPool_std_allocator_std_shared_ptr_protocols_frag_picker_quota_QuotaPool_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_AdaptiveScoreHistogram_std_allocator_std_shared_ptr_protocols_frag_picker_scores_AdaptiveScoreHistogram_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_AtomPairConstraintsData_std_allocator_std_shared_ptr_protocols_frag_picker_scores_AtomPairConstraintsData_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_FourAtomsConstraintData_std_allocator_std_shared_ptr_protocols_frag_picker_scores_FourAtomsConstraintData_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_Entity_std_allocator_std_shared_ptr_protocols_genetic_algorithm_Entity_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_std_allocator_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_protocols_jd3_JGJobNode_std_allocator_std_shared_ptr_protocols_jd3_JGJobNode_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_protocols_minimization_packing_MinimalRotamer_std_allocator_std_shared_ptr_protocols_minimization_packing_MinimalRotamer_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_shared_ptr_protocols_pose_sewing_data_storage_SegmentEnvelope_std_allocator_std_shared_ptr_protocols_pose_sewing_data_storage_SegmentEnvelope_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_std_string_std_allocator_std_string_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_utility_keys_Key2Tuple_unsigned_long_unsigned_long_std_allocator_utility_keys_Key2Tuple_unsigned_long_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_utility_keys_Key3Tuple_unsigned_long_unsigned_long_unsigned_long_std_allocator_utility_keys_Key3Tuple_unsigned_long_unsigned_long_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_std_allocator_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_std_allocator_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_std_allocator_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_std_allocator_utility_vector1_unsigned_long_std_allocator_unsigned_long_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.utility) vector1_utility_vector1_void__star__std_allocator_void__star__t (class in pyrosetta.rosetta.utility) vector_angle_cut() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.protocols.simple_filters.DomainInterfaceFilter method) vector_angle_cutoff() (pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) vector_core_io_AtomInformation (class in pyrosetta.rosetta.std) vector_core_io_RemarkInfo (class in pyrosetta.rosetta.std) vector_core_pose_Pose (class in pyrosetta.rosetta.std) vector_core_scoring_hbonds_graph_HBondInfo (class in pyrosetta.rosetta.std) vector_core_scoring_sc__DOT (class in pyrosetta.rosetta.std) vector_core_scoring_sc_Atom (class in pyrosetta.rosetta.std) vector_dist_cut() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.protocols.simple_filters.DomainInterfaceFilter method) vector_dist_cutoff() (pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) vector_double (class in pyrosetta.rosetta.std) vector_float (class in pyrosetta.rosetta.std) vector_has_n_trues() (in module pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster) vector_int (class in pyrosetta.rosetta.std) vector_normal_to_ring_plane_of_best_fit() (in module pyrosetta.rosetta.numeric.geometry) vector_numeric_xyzMatrix_double_t (class in pyrosetta.rosetta.std) vector_numeric_xyzVector_double_t (class in pyrosetta.rosetta.std) vector_protocols_cluster_Cluster (class in pyrosetta.rosetta.std) vector_protocols_motif_grafting_movers_MotifMatch (class in pyrosetta.rosetta.std) vector_RDGeom_Point3D (class in pyrosetta.rosetta.std) vector_RDKit_Dict_Pair (class in pyrosetta.rosetta.std) vector_std_list_std_shared_ptr_const_core_conformation_Residue_t (class in pyrosetta.rosetta.std) vector_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t (class in pyrosetta.rosetta.std) vector_std_map_unsigned_long_unsigned_long_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_unsigned_long_t (class in pyrosetta.rosetta.std) vector_std_pair_std_shared_ptr_protocols_filters_Filter_protocols_filters_boolean_operations_t (class in pyrosetta.rosetta.std) vector_std_pair_unsigned_long_unsigned_long_t (class in pyrosetta.rosetta.std) vector_std_set_unsigned_long_t (class in pyrosetta.rosetta.std) vector_std_shared_ptr_const_core_conformation_Residue_t (class in pyrosetta.rosetta.std) vector_std_shared_ptr_core_chemical_Orbital_t (class in pyrosetta.rosetta.std) vector_std_shared_ptr_core_fragment_FragSet_t (class in pyrosetta.rosetta.std) vector_std_shared_ptr_core_io_silent_SilentStruct_t (class in pyrosetta.rosetta.std) vector_std_shared_ptr_core_pose_Pose_t (class in pyrosetta.rosetta.std) vector_std_shared_ptr_protocols_cluster_calibur_Stru_t (class in pyrosetta.rosetta.std) vector_std_shared_ptr_protocols_hbnet_HBondNetStruct_t (class in pyrosetta.rosetta.std) vector_std_shared_ptr_std_list_std_shared_ptr_const_utility_tag_Tag_t (class in pyrosetta.rosetta.std) vector_std_string (class in pyrosetta.rosetta.std) vector_std_vector_double_std_allocator_double_t (in module pyrosetta.rosetta.std) vector_std_vector_double_t (class in pyrosetta.rosetta.std) vector_std_vector_int_t (class in pyrosetta.rosetta.std) vector_std_vector_std_string_t (class in pyrosetta.rosetta.std) vector_std_vector_std_vector_double_t (class in pyrosetta.rosetta.std) vector_std_vector_unsigned_long_t (class in pyrosetta.rosetta.std) vector_to_rank() (in module pyrosetta.rosetta.protocols.ligand_docking) vector_unsigned_int (class in pyrosetta.rosetta.std) vector_unsigned_long (class in pyrosetta.rosetta.std) vector_utility_file_FileName (class in pyrosetta.rosetta.std) vector_utility_json_spirit_Pair_impl_utility_json_spirit_Config_vector_std_string_t (class in pyrosetta.rosetta.std) vector_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t (class in pyrosetta.rosetta.std) vector_utility_json_spirit_Value_impl_utility_json_spirit_Config_vector_std_string_t (class in pyrosetta.rosetta.std) vector_utility_signals_Link (class in pyrosetta.rosetta.std) vector_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.std) vector_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t (class in pyrosetta.rosetta.std) vector_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t (class in pyrosetta.rosetta.std) vector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t (class in pyrosetta.rosetta.std) vector_values() (pyrosetta.rosetta.protocols.pack_daemon.IterativeVectorExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VariableVectorExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VectorExpression method) VectorExpression (class in pyrosetta.rosetta.protocols.pack_daemon) VectorExpressionCreator (class in pyrosetta.rosetta.protocols.pack_daemon) VectorFunction (class in pyrosetta.rosetta.protocols.pack_daemon) VectorFunction2 (class in pyrosetta.rosetta.protocols.pack_daemon) vectorL_IndexSelector_false_t (class in pyrosetta.rosetta.utility) vectorL_IndexSelector_true_t (class in pyrosetta.rosetta.utility) vectorL_ZeroSelector_false_t (class in pyrosetta.rosetta.utility) vectorL_ZeroSelector_true_t (class in pyrosetta.rosetta.utility) VectorOption (class in pyrosetta.rosetta.utility.options) VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t (class in pyrosetta.rosetta.utility.options) VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t (class in pyrosetta.rosetta.utility.options) VectorOption_T_utility_options_IntegerVectorOptionKey_int_t (class in pyrosetta.rosetta.utility.options) VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t (class in pyrosetta.rosetta.utility.options) VectorOption_T_utility_options_RealVectorOptionKey_double_t (class in pyrosetta.rosetta.utility.options) VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t (class in pyrosetta.rosetta.utility.options) VectorOption_T_utility_options_StringVectorOptionKey_std_string_t (class in pyrosetta.rosetta.utility.options) VectorOptionKey (class in pyrosetta.rosetta.utility.options) VectorPair (class in pyrosetta.rosetta.protocols.hotspot_hashing) VectorPoseFilter (class in pyrosetta.rosetta.protocols.filters) VectorPoseJobDistributor (class in pyrosetta.rosetta.protocols.jd2) VectorPoseMover (class in pyrosetta.rosetta.protocols.moves) VectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t (class in pyrosetta.rosetta.protocols.denovo_design.components) vectorsEqual() (in module pyrosetta.rosetta.numeric.kinematic_closure) vecx (pyrosetta.rosetta.protocols.loophash.LegacyLeapIndex property) vecy (pyrosetta.rosetta.protocols.loophash.LegacyLeapIndex property) vecz (pyrosetta.rosetta.protocols.loophash.LegacyLeapIndex property) vel() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) velocity (pyrosetta.rosetta.protocols.cartesian.CartesianAtom property) ver() (pyrosetta.rosetta.utility.file.FileName method) verbose() (pyrosetta.rosetta.core.import_pose.options.RNA_BasicOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric method) (pyrosetta.rosetta.protocols.fldsgn.filters.InterlockingAromaFilter method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilter method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter method) (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilter method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.StepWiseSampleAndScreen method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) verbose_ (pyrosetta.rosetta.protocols.stepwise.StepWiseSampleAndScreen property) verbose_sampler() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) verbose_scores() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) verify_against() (pyrosetta.rosetta.protocols.loops.Loops method) Version (class in pyrosetta.rosetta.utility) version() (in module pyrosetta) (pyrosetta.rosetta.core.energy_methods.AACompositionEnergy method) (pyrosetta.rosetta.core.energy_methods.AARepeatEnergy method) (pyrosetta.rosetta.core.energy_methods.Abego method) (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.BranchEnergy method) (pyrosetta.rosetta.core.energy_methods.Burial_v2Energy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CCS_IMMSEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifDegreeEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.ChemicalShiftAnisotropyEnergy method) (pyrosetta.rosetta.core.energy_methods.ContactOrderEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.D2H_SA_Energy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.energy_methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FastSAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyDens method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HolesEnergy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.IntermolEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.LoopCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvPenalties method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneLipo method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergy method) (pyrosetta.rosetta.core.energy_methods.MissingEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.OtherPoseEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.PackStatEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.ProQ_Energy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy_Rohl method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_Fast method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_RNA method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergy method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RMS_Energy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalMappingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PartitionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SA_Energy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCreatorCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCreatorFA method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) (pyrosetta.rosetta.core.energy_methods.SecondaryStructureEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfVolEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.XtalMLEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.io.rna.RDAT method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomePackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.packing.HolesEnergyRes method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.features.ProteinSilentReport method) (pyrosetta.rosetta.protocols.features.Report method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergy method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.EnsembleEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.ResidualDipolarCouplingEnergyRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergy method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy method) (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) (pyrosetta.rosetta.protocols.sewing.hashing.EdgeMapGenerator method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.Version static method) vertex() (pyrosetta.rosetta.core.chemical.MutableResidueConnection method) vertex_already_reached() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) vertex_count() (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) (pyrosetta.rosetta.core.scoring.SASAPotential method) vertex_exists() (in module pyrosetta.rosetta.protocols.forge.methods) vertex_xyz_from_generators() (in module pyrosetta.rosetta.core.scoring.power_diagram) vertices() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) very_far_away() (pyrosetta.rosetta.protocols.symmetry.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SymmetrySlider method) Vesicle (class in pyrosetta.rosetta.core.conformation.membrane.membrane_geometry) VESICLE (pyrosetta.rosetta.core.conformation.membrane.MP_GEOMETRY_TRANSITION attribute) VH_sheet_1 (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum attribute) VH_sheet_2 (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum attribute) VicinityPerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) VicinitySamplingKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) view() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) view_constraints_in_pymol() (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) violates() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalLengthRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyIntraSegmentRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementSet method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyResidueRetentionRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentDsspRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentLengthRequirement method) viols() (pyrosetta.rosetta.core.scoring.func.CountViolFunc method) (pyrosetta.rosetta.core.scoring.func.SkipViolFunc method) VIP_Mover (class in pyrosetta.rosetta.protocols.vip) VIP_Report (class in pyrosetta.rosetta.protocols.vip) VirtResClaim (class in pyrosetta.rosetta.protocols.environment.claims) virtual_anchor_attachment_points() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) virtual_anomeric_carbon_index() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) VIRTUAL_ATOM (pyrosetta.rosetta.core.chemical.AtomProperty attribute) VIRTUAL_BACKBONE_EXCEPT_C1PRIME (pyrosetta.rosetta.core.chemical.VariantType attribute) VIRTUAL_BASE (pyrosetta.rosetta.core.chemical.VariantType attribute) VIRTUAL_BASE_HEAVY_ATOM (pyrosetta.rosetta.core.chemical.VariantType attribute) VIRTUAL_BB (pyrosetta.rosetta.core.chemical.VariantType attribute) virtual_cyclic_oxygen_index() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) VIRTUAL_DNA_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) VIRTUAL_METAL_CONJUGATION (pyrosetta.rosetta.core.chemical.VariantType attribute) VIRTUAL_NTERM (pyrosetta.rosetta.core.chemical.VariantType attribute) VIRTUAL_O2PRIME_HYDROGEN (pyrosetta.rosetta.core.chemical.VariantType attribute) VIRTUAL_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) VIRTUAL_RESIDUE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) VIRTUAL_RESIDUE_VARIANT (pyrosetta.rosetta.core.chemical.VariantType attribute) VIRTUAL_RIBOSE (pyrosetta.rosetta.core.chemical.VariantType attribute) VIRTUAL_RNA_RESIDUE (pyrosetta.rosetta.core.chemical.VariantType attribute) VIRTUAL_RNA_RESIDUE_EXCLUDE_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) VIRTUAL_SIDE_CHAIN (pyrosetta.rosetta.core.chemical.VariantType attribute) virtual_sidechain() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) virtual_sugar_do_minimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) virtual_sugar_do_screens() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) virtual_sugar_keep_base_fixed() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) virtual_sugar_legacy_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) virtual_to_real() (pyrosetta.rosetta.core.pose.Pose method) virtual_type_for_conf() (in module pyrosetta.rosetta.core.conformation) virtual_type_for_pose() (in module pyrosetta.rosetta.core.pose) VirtualCoordinate (class in pyrosetta.rosetta.core.conformation.symmetry) VIRTUALIZABLE_BY_PACKER (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) virtualize_5prime_phosphates() (in module pyrosetta.rosetta.core.pose.rna) virtualize_bulges() (in module pyrosetta.rosetta.protocols.rna.denovo) virtualize_free_rna_moieties() (in module pyrosetta.rosetta.core.pose.rna) virtualize_packable_moieties_in_screening_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) virtualize_side_chains() (in module pyrosetta.rosetta.protocols.stepwise.modeler) VirtualizeAll (class in pyrosetta.rosetta.core.chemical) VirtualizeSidechain (class in pyrosetta.rosetta.core.chemical) VirtualResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) VirtualResidueSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) VirtualRootMover (class in pyrosetta.rosetta.protocols.simple_moves) VirtualRootMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) VirtualSugarJustInTimeInstantiator (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) VirtualSugarSampler (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) VirtualSugarSamplerFromStringList (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) visible() (pyrosetta.rosetta.basic.MemTracer method) (pyrosetta.rosetta.basic.MemTracer.TracerProxy method) (pyrosetta.rosetta.basic.MemTracerImpl method) (pyrosetta.rosetta.basic.MemTracerImpl.TracerProxyImpl method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.Tracer.TracerProxy method) (pyrosetta.rosetta.basic.TracerImpl method) (pyrosetta.rosetta.basic.TracerImpl.TracerProxyImpl method) visit() (pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTAndClause method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTExpression method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTFactor method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTFunction method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTOrClause method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestAndClause method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestExpression method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestOrClause method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestTerm method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTTerm method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter method) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor method) (pyrosetta.rosetta.numeric.expression_parser.BooleanExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.SimpleExpressionCreator method) (pyrosetta.rosetta.numeric.geometry.hashing.Counter method) (pyrosetta.rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator method) (pyrosetta.rosetta.protocols.pack_daemon.EntityFuncExpressionCreator method) (pyrosetta.rosetta.protocols.pack_daemon.VectorExpressionCreator method) visit_next_leaf() (pyrosetta.rosetta.numeric.ClusteringTreeNode method) visited() (pyrosetta.rosetta.core.environment.FoldTreeSketch.Node method) visualize_at_depth() (pyrosetta.rosetta.core.scoring.atomic_depth.AtomicDepth method) visualize_fold_tree() (in module pyrosetta.rosetta.core.kinematics) visualize_voxel_grid() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) VisualizeEmbeddingMover (class in pyrosetta.rosetta.protocols.membrane.visualize) VisualizeEmbeddingMoverCreator (class in pyrosetta.rosetta.protocols.membrane.visualize) VisualizeMembraneMover (class in pyrosetta.rosetta.protocols.membrane.visualize) VisualizeMembraneMoverCreator (class in pyrosetta.rosetta.protocols.membrane.visualize) VL_sheet_1 (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum attribute) VL_sheet_2 (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum attribute) vl_vh_cut() (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) vl_vh_orientation_coords() (in module pyrosetta.rosetta.protocols.antibody) VLB (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) vlb() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) VLBCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) VLBInstruction (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) VLBInstructionType (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) VLBProtected (class in pyrosetta.rosetta.protocols.denovo_design.components) VMax (class in pyrosetta.rosetta.protocols.pack_daemon) vmax_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) VMaxBy (class in pyrosetta.rosetta.protocols.pack_daemon) VMin (class in pyrosetta.rosetta.protocols.pack_daemon) vmin_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) VMinBy (class in pyrosetta.rosetta.protocols.pack_daemon) voids_penalty (pyrosetta.rosetta.core.scoring.ScoreType attribute) voids_penalty_energy_cone_distance_cutoff() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) voids_penalty_energy_cone_dotproduct_cutoff() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) voids_penalty_energy_containing_cones_cutoff() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) voids_penalty_energy_disabled_except_during_packing() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) voids_penalty_energy_voxel_grid_padding() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) voids_penalty_energy_voxel_size() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) VoidsPenaltyEnergy (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy) VoidsPenaltyEnergyCreator (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy) VoidsPenaltyVoxelGrid (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy) vol (pyrosetta.rosetta.core.scoring.packing.SurfVol property) (pyrosetta.rosetta.core.scoring.packing.SurfVolDeriv property) (pyrosetta.rosetta.core.scoring.packstat.CavityBall property) vol() (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) volume (pyrosetta.rosetta.core.scoring.packstat.CavityBallCluster property) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData property) volume() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) volume_issue_pages() (pyrosetta.rosetta.basic.citation_manager.Citation method) volumepixel (class in pyrosetta.rosetta.core.scoring.atomic_depth) voxel (class in pyrosetta.rosetta.core.scoring.atomic_depth) voxel2 (class in pyrosetta.rosetta.core.scoring.atomic_depth) VoxelGridPoint (class in pyrosetta.rosetta.core.scoring.nmr) VoxelGridPoint_AA (class in pyrosetta.rosetta.core.scoring.nmr) VoxelSetIterator (class in pyrosetta.rosetta.protocols.match) VoxelSpacingMultifunc (class in pyrosetta.rosetta.protocols.electron_density) VoxelSpacingRefinementMover (class in pyrosetta.rosetta.protocols.electron_density) VoxelSpacingRefinementMoverCreator (class in pyrosetta.rosetta.protocols.electron_density) VRT1 (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) vrt1() (pyrosetta.rosetta.core.scoring.PDinter method) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) vrt2() (pyrosetta.rosetta.core.scoring.PDinter method) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) vrt_label() (pyrosetta.rosetta.protocols.environment.claims.VirtResClaim method) vvr_hotspots (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data property)